Workflow

Detailed software versions can be found under Rules.

Results

File Size Description Job properties
simulated-bwa.DEL.svg 328.3 kB

Allele frequency estimation error vs. true allele frequency on simulated data.

Ruleplot_allelefreq
Wildcardsrun=simulated-bwa, vartype=DEL
Paramsvarlociraptor_callers=['delly', 'lancet', 'manta', 'strelka'], len_ranges=[[1, 30], [30, 50], [50, 100], [100, 250]]
simulated-bwa.DEL.svg 1.9 MB

Allele frequency estimation error vs. true allele frequency on simulated data. The dashed lines depict the standard deviation, solid line depicts the mean. The grey area shows the standard deviation of a corresponding binomial sampling, which marks the maximum theoretically achievable accuracy.

Ruleplot_allelefreq_scatter
Wildcardsrun=simulated-bwa, vartype=DEL
Paramsdepth_ranges=[[1, 20], [20, 40]], callers=['delly', 'lancet', 'manta', 'strelka']
simulated-bwa.INS.svg 185.2 kB

Allele frequency estimation error vs. true allele frequency on simulated data.

Ruleplot_allelefreq
Wildcardsrun=simulated-bwa, vartype=INS
Paramsvarlociraptor_callers=['delly', 'lancet', 'manta', 'strelka'], len_ranges=[[1, 30], [30, 100]]
simulated-bwa.INS.svg 2.1 MB

Allele frequency estimation error vs. true allele frequency on simulated data. The dashed lines depict the standard deviation, solid line depicts the mean. The grey area shows the standard deviation of a corresponding binomial sampling, which marks the maximum theoretically achievable accuracy.

Ruleplot_allelefreq_scatter
Wildcardsrun=simulated-bwa, vartype=INS
Paramsdepth_ranges=[[1, 10], [10, 20], [20, 40], [40, 100]], callers=['delly', 'lancet', 'manta', 'strelka']
File Size Description Job properties
colo1.DEL.concordance.svg 563.4 kB

For concordance analysis, we ran varlociraptor and the other callers on four independent sequencings of the same tumor/normal pair. Called variants were matched against each other, yielding a graph. Connected components in this graph of more than one node we counted as concordant calls. Left plot shows concordance vs minimum allele frequency. Right plot shows number of calls vs minimum allele frequency. For Varlociraptor, results are shown as area between a minimum posterior probability (for somatic in tumor) of 0.9 and 0.98. For all other callers, results are shown as dotted lines (obtained with default parameters). The grey lines depict the theoretical expectation according to the model of neutral tumor evolution by Williams et al. See paper for details.

Ruleplot_concordance
Wildcardsid=colo1, vartype=DEL
Paramscallers=['delly', 'lancet', 'manta', 'strelka', 'bpi']
colo1.INS.concordance.svg 428.9 kB

For concordance analysis, we ran varlociraptor and the other callers on four independent sequencings of the same tumor/normal pair. Called variants were matched against each other, yielding a graph. Connected components in this graph of more than one node we counted as concordant calls. Left plot shows concordance vs minimum allele frequency. Right plot shows number of calls vs minimum allele frequency. For Varlociraptor, results are shown as area between a minimum posterior probability (for somatic in tumor) of 0.9 and 0.98. For all other callers, results are shown as dotted lines (obtained with default parameters). The grey lines depict the theoretical expectation according to the model of neutral tumor evolution by Williams et al. See paper for details.

Ruleplot_concordance
Wildcardsid=colo1, vartype=INS
Paramscallers=['delly', 'lancet', 'manta', 'strelka', 'bpi']
File Size Description Job properties
simulated-bwa.DEL.svg 77.8 kB

Performance of FDR control on simulated data. Horizontal axis shows the applied FDR threshold, vertical axis shows the true FDR of the selected set of variants. Perfect FDR control would result in a line directly on the diagonal. Conservative control would lie in the area below the diagonal. Anything above the diagonal would be overly optimistic.

Ruleplot_fdr
Wildcardsrun=simulated-bwa, vartype=DEL
Paramscallers=['delly', 'lancet', 'manta', 'strelka'], purity=0.75, len_ranges=[[1, 30], [30, 50], [50, 100], [100, 250]], fdrs=[1e-05, 0.0001, 0.001, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
simulated-bwa.INS.svg 52.1 kB

Performance of FDR control on simulated data. Horizontal axis shows the applied FDR threshold, vertical axis shows the true FDR of the selected set of variants. Perfect FDR control would result in a line directly on the diagonal. Conservative control would lie in the area below the diagonal. Anything above the diagonal would be overly optimistic.

Ruleplot_fdr
Wildcardsrun=simulated-bwa, vartype=INS
Paramscallers=['delly', 'lancet', 'manta', 'strelka'], purity=0.75, len_ranges=[[1, 30], [30, 100]], fdrs=[1e-05, 0.0001, 0.001, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
File Size Description Job properties
simulated-bwa.DEL.svg 100.9 kB

Precision and recall on simulated data.

Ruleplot_precision_recall
Wildcardsrun=simulated-bwa, vartype=DEL
Paramsvarlociraptor_callers=['delly', 'lancet', 'manta', 'strelka'], default_callers=['lancet', 'manta', 'strelka'], adhoc_callers=['delly', 'lancet', 'manta', 'strelka', 'bpi'], len_ranges=[[1, 30], [30, 50], [50, 100], [100, 250]]
simulated-bwa.INS.svg 63.0 kB

Precision and recall on simulated data.

Ruleplot_precision_recall
Wildcardsrun=simulated-bwa, vartype=INS
Paramsvarlociraptor_callers=['delly', 'lancet', 'manta', 'strelka'], default_callers=['lancet', 'manta', 'strelka'], adhoc_callers=['delly', 'lancet', 'manta', 'strelka', 'bpi'], len_ranges=[[1, 30], [30, 100]]
File Size Description Job properties
simulated-bwa.DEL.svg 114.6 kB

Distribution of true and false positives depending on posterior probability for somatic variant in the tumor as given by varlociraptor. Desirable is a good separation between the two distributions.

Ruleplot_score_dist
Wildcardsrun=simulated-bwa, vartype=DEL
Paramsvarlociraptor_callers=['delly', 'lancet', 'manta', 'strelka'], len_ranges=[[1, 30], [30, 50], [50, 100], [100, 250]]
simulated-bwa.INS.svg 79.1 kB

Distribution of true and false positives depending on posterior probability for somatic variant in the tumor as given by varlociraptor. Desirable is a good separation between the two distributions.

Ruleplot_score_dist
Wildcardsrun=simulated-bwa, vartype=INS
Paramsvarlociraptor_callers=['delly', 'lancet', 'manta', 'strelka'], len_ranges=[[1, 30], [30, 100]]

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

File Code
config.yaml
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gdc-manifest: gdc_manifest_20171012_060907.txt

runs:
  simulated-bwa:
    mapper: bwa
    dataset: simulated
    ref: hg18
    purity: 0.75
  COLO_829-GSC:
    dataset: COLO_829-GSC
    mapper: bwa
    ref: hg38
    purity: 1.0
  COLO_829-EBI:
    dataset: COLO_829-EBI
    mapper: bwa
    ref: hg38
    purity: 1.0
  COLO_829-TGen:
    dataset: COLO_829-TGen
    mapper: bwa
    ref: hg38
    purity: 1.0
  COLO_829-Ill:
    dataset: COLO_829-Ill
    mapper: bwa
    ref: hg38
    purity: 1.0


datasets:
  simulated:
    tumor:
      bam: ../data/hiseq.Cancer80.wholegenome.bwamemm.cat.sorted.smtag.bam
      name: Cancer80
    normal:
      bam: ../data/hiseq.Control.wholegenome.cov30.bwamemm.sorted.smtag.bam
      name: Control
    isize:
      mean: 312
      sd: 15
    truth: ../data/simulated-truth.indels.vcf
  COLO_829-GSC:
    tumor:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001226259_COLO_829_BCGSC_BCGSCPipe.bam
      name: Cancer
    normal:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001226245_COLO_829BL_BCGSC_BCGSCPipe.bam
      name: Control
    case: COLO_829
  COLO_829-EBI:
    tumor:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001226269_COLO_829_EPleasance_BCGSCPipe.bam
      name: Cancer
    normal:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001226254_COLO_829BL_EPleasance_BCGSCPipe.bam
      name: Control
    case: COLO_829
  COLO_829-Ill:
    tumor:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001226270_COLO_829_Illumina_BCGSCPipe.bam
      name: Cancer
    normal:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001226256_COLO_829BL_Illumina_BCGSCPipe.bam
      name: Control
    case: COLO_829
  COLO_829-TGen:
    tumor:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001229972_COLO_829_TGEN_BCGSCPipe.bam
      name: Cancer
    normal:
      bam: ../data/EGAD00001002142/EGAD00001002142/EGAZ00001226249_COLO_829BL_TGEN_BCGSCPipe.bam
      name: Control
    case: COLO_829

ref:
  hg18:
    fasta: ../data/hg18.fasta
    date: 2006-03
    chrom_prefix: chr
  hg38:
    fasta: ../data/Homo_sapiens.GRCh38.dna.primary_assembly.fa
    date: 2013-12
    chrom_prefix: ""
    exons: resources/hg38.exons.bed

caller:
  delly:
    params: ""
    adhoc: true
    genotypes: true
    info:
      - END
      - SOMATIC
      - SVLEN
      - SVTYPE
  #pindel:
  #  params: "-M 1 -B 10000 -H 10 -x 4 -I false -a 2"
  lancet:
    params: ""
    score: QUAL
    invert: true
    adhoc: true
    genotypes: true
    info:
      - SOMATIC
      - SVLEN
      - SVTYPE
  manta:
    params: ""
    score: SOMATICSCORE
    invert: true
    adhoc: true
    useraw: true
    info:
      - SOMATIC
      - SOMATICSCORE
      - SVLEN
      - SVTYPE
  strelka:
    params: ""
    score: QSI
    invert: true
    adhoc: true
    info:
      - SOMATIC
      - QSI
  bpi:
    params: ""
    adhoc: true
    info:
      - SOMATIC
      - SVLEN
      - SVTYPE
  varlociraptor:
    params: "--indel-window 64 --omit-snvs"
    blacklist:
      - bpi
    score: PROB_SOMATIC_TUMOR
    genotypes: false
    info:
      - PROB_SOMATIC_TUMOR
      - PROB_GERMLINE_HET
      - PROB_GERMLINE_HOM
      - PROB_ABSENT
      - PROB_SOMATIC_NORMAL
      - PROB_ARTIFACT
      - SVLEN
    fmt:
      - AF
      - DP

vcf-match-params: "--max-dist 50 --max-len-diff 50"

len-ranges:
  DEL:
    - [1, 30]
    - [30, 50]
    - [50, 100]
    - [100, 250]
  INS:
    - [1, 30]
    - [30, 100]


depth-ranges:
  DEL:
    - [1, 20]
    - [20, 40]
  INS:
    - [1, 10]
    - [10, 20]
    - [20, 40]
    - [40, 100]


plots:
  concordance:
    colo1:
      - COLO_829-GSC
      - COLO_829-Ill
      - COLO_829-TGen
      - COLO_829-EBI
  known-truth:
    - simulated-bwa

Rules

Rule Jobs Output Singularity Conda environment Code
plot_precision_recall 2
  • plots/precision-recall/simulated-bwa.INS.svg
  • plots/precision-recall/simulated-bwa.DEL.svg
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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from itertools import product
import matplotlib
matplotlib.use("agg")
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import common
import numpy as np
import math
from matplotlib.lines import Line2D

MIN_CALLS = 10

vartype = snakemake.wildcards.vartype
colors = common.get_colors(snakemake.config)


def props(callers):
    return product(callers, snakemake.params.len_ranges)


def plot_len_range(minlen, maxlen):

    truth = common.load_variants(
        snakemake.input.truth, minlen, maxlen, vartype=vartype)

    def plot(calls,
             label,
             color,
             line=True,
             style="-",
             invert=False,
             markersize=4):
        calls = pd.read_table(calls, index_col=0)
        if len(calls) < 10:
            return
        if line:
            thresholds = calls.score.quantile(np.linspace(0.0, 1.0, 50))
            precision = []
            recall = []
            for t in thresholds:
                if invert:
                    c = calls[calls.score >= t]
                else:
                    c = calls[calls.score <= t]
                p = common.precision(c)
                r = common.recall(c, truth)
                print(label, t, c.shape[0], p, r)
                if len(c) < 10:
                    print("skipping threshold: too few calls", c)
                    continue
                precision.append(p)
                recall.append(r)
            if len(precision) <= 2:
                print("skipping curve because we have too few values")
                return
        else:
            precision = [common.precision(calls)]
            recall = [common.recall(calls, truth)]
            style = "."
            print(label, calls.shape[0], precision, recall)
        plt.plot(
            recall,
            precision,
            style,
            color=color,
            label=label,
            markersize=markersize)

    handles = []
    for calls, (caller,
                len_range) in zip(snakemake.input.varlociraptor_calls,
                                  props(snakemake.params.varlociraptor_callers)):
        if len_range[0] != minlen and len_range[1] != maxlen:
            continue
        label = "varlociraptor+{}".format(caller)
        plot(calls, label, colors[caller])
        handles.append(Line2D([0], [0], color=colors[caller], label=label))

    for calls, (caller,
                len_range) in zip(snakemake.input.default_calls,
                                  props(snakemake.params.default_callers)):
        if len_range[0] != minlen and len_range[1] != maxlen:
            continue
        color = colors[caller]
        plot(
            calls,
            caller,
            color,
            style=":",
            invert=snakemake.config["caller"][caller].get("invert", False))
        if caller in snakemake.params.adhoc_callers:
            handles.append(Line2D([0], [0], markersize=10, markerfacecolor=color, markeredgecolor=color, color=color, label=caller, marker=".", linestyle=":"))
        else:
            handles.append(Line2D([0], [0], color=color, label=caller, linestyle=":"))

    for calls, (caller, len_range) in zip(snakemake.input.adhoc_calls,
                             props(snakemake.params.adhoc_callers)):
        if len_range[0] != minlen and len_range[1] != maxlen:
            continue
        color = colors[caller]
        plot(calls, caller, color, markersize=10, line=False)
        if caller not in snakemake.params.default_callers:
            handles.append(Line2D([0], [0], markersize=10, markerfacecolor=color, markeredgecolor=color, label=caller, marker=".", lw=0))

    sns.despine()
    ax = plt.gca()
    return ax, handles


common.plot_ranges(
    snakemake.params.len_ranges,
    plot_len_range,
    xlabel="recall",
    ylabel="precision")

plt.savefig(snakemake.output[0], bbox_inches="tight")
svg2pdf 14
  • plots/precision-recall/simulated-bwa.INS.pdf
  • plots/precision-recall/simulated-bwa.DEL.pdf
  • plots/fdr-control/simulated-bwa.INS.pdf
  • plots/fdr-control/simulated-bwa.DEL.pdf
  • plots/allelefreqs/simulated-bwa.INS.pdf
  • plots/allelefreqs/simulated-bwa.DEL.pdf
  • plots/score-dist/simulated-bwa.INS.pdf
  • plots/score-dist/simulated-bwa.DEL.pdf
  • plots/allelefreq-recall/simulated-bwa.INS.pdf
  • plots/allelefreq-recall/simulated-bwa.DEL.pdf
  • plots/allelefreq-scatter/simulated-bwa.INS.pdf
  • plots/allelefreq-scatter/simulated-bwa.DEL.pdf
  • plots/concordance/colo1.INS.concordance.pdf
  • plots/concordance/colo1.DEL.concordance.pdf
  • cairosvg =2.1.3
1
cairosvg {input} -o {output}
plot_fdr 2
  • plots/fdr-control/simulated-bwa.INS.svg
  • plots/fdr-control/simulated-bwa.DEL.svg
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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from itertools import product
import matplotlib
matplotlib.use("agg")
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import common
import numpy as np


MIN_CALLS = 100

colors = common.get_colors(snakemake.config)

props = product(snakemake.params.callers,
                snakemake.params.len_ranges, snakemake.params.fdrs)

calls = []

for _calls, (caller, len_range, fdr) in zip(snakemake.input.varlociraptor_calls, props):
    calls.append({"caller": caller, "len_range": len_range, "fdr": float(fdr), "calls": _calls})

calls = pd.DataFrame(calls)
calls = calls.set_index("caller", drop=False)


def plot_len_range(minlen, maxlen):

    def plot(caller):
        color = colors[caller]
        label = "varlociraptor+{}".format(caller)
        fdrs = []
        alphas = []
        calls_ = calls.loc[caller]
        calls_ = calls_[calls_["len_range"].map(lambda r: r == [minlen, maxlen])]
        calls_ = calls_.sort_values("fdr")
        for e in calls_.itertuples():
            c = pd.read_table(e.calls)
            n = c.shape[0]
            if n < MIN_CALLS:
                continue
            true_fdr = 1.0 - common.precision(c)
            if fdrs and fdrs[-1] == true_fdr:
                continue
            fdrs.append(true_fdr)
            alphas.append(e.fdr)
        plt.plot(alphas, fdrs, ".-", color=color, label=label)


    for caller in calls.index.unique():
        plot(caller)

    plt.plot([0, 1], [0, 1], ":", color="grey")

    sns.despine()
    ax = plt.gca()
    handles, _ = ax.get_legend_handles_labels()
    return ax, handles

common.plot_ranges(
    snakemake.params.len_ranges,
    plot_len_range,
    xlabel="FDR threshold",
    ylabel="true FDR")

plt.savefig(snakemake.output[0], bbox_inches="tight")
plot_allelefreq 2
  • plots/allelefreqs/simulated-bwa.INS.svg
  • plots/allelefreqs/simulated-bwa.DEL.svg
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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from itertools import product
import math
import matplotlib
matplotlib.use("agg")
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import common
import numpy as np


MIN_CALLS = 10

vartype = snakemake.wildcards.vartype
colors = common.get_colors(snakemake.config)

truth = common.load_variants(snakemake.input.truth, vartype=vartype)

def props(callers):
    return product(callers, snakemake.params.len_ranges)

def plot_len_range(minlen, maxlen):
    def plot(calls, colors):
        calls = calls[calls.is_tp]
        true_af = truth.loc[calls.MATCHING].reset_index().TAF
        calls = calls.reset_index()
        calls["error"] = calls.CASE_AF - true_af

        if calls.empty:
            return

        calls["true_af"] = true_af
        true_af = pd.Series(calls["true_af"].unique()).sort_values()
        # standard deviation when sampling in binomial process from allele freq
        # this is the expected sampling error within the correctly mapped fragments
        # sd = true_af.apply(lambda af: 1 / 40 * math.sqrt(40 * af * (1 - af)))
        # x = np.arange(len(true_af))
        # offsets = [-0.5, 0.5]
        # y_upper = np.array([v for v in sd for o in offsets])
        #  y_lower = np.maximum(-y_upper, [-f for f in true_af for o in offsets])
        # plt.fill_between([v + o for v in x for o in offsets], y_lower, y_upper, color="#EEEEEE", zorder=-5)

        calls["true_af"] = calls["true_af"].apply("{:.3f}".format)

        size = 1 if maxlen == 30 else 2
        sns.stripplot("true_af", "error", hue="caller", data=calls, palette=colors, dodge=True, jitter=True, alpha=0.5, size=size, rasterized=True)
        sns.boxplot("true_af", "error", hue="caller", data=calls, color="white", fliersize=0, linewidth=1)

        handles, labels = plt.gca().get_legend_handles_labels()
        n = len(calls.caller.unique())

        plt.ylim((-1,1))
        plt.grid(axis="y", linestyle=":", color="grey")
        sns.despine()
        plt.xticks(rotation="vertical")
        ax = plt.gca()
        ax.legend().remove()

        return ax, handles[n:]

    all_calls, all_colors = load_calls(minlen, maxlen)
    return plot(all_calls, all_colors)

def load_calls(minlen, maxlen):
    all_calls = []
    all_colors = []
    for calls, (caller, len_range) in zip(snakemake.input.varlociraptor_calls, props(snakemake.params.varlociraptor_callers)):
        if len_range[0] != minlen and len_range[1] != maxlen:
            continue
        label = "varlociraptor+{}".format(caller)
        calls = pd.read_table(calls)
        calls["caller"] = label
        if not calls.empty:
            all_calls.append(calls)
            all_colors.append(colors[caller])

    all_calls = pd.concat(all_calls)
    return all_calls, all_colors

common.plot_ranges(
    snakemake.params.len_ranges,
    plot_len_range,
    xlabel="true allele frequency",
    ylabel="predicted - truth")

plt.savefig(snakemake.output[0], bbox_inches="tight")
plot_score_dist 2
  • plots/score-dist/simulated-bwa.INS.svg
  • plots/score-dist/simulated-bwa.DEL.svg
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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from itertools import product
import matplotlib
matplotlib.use("agg")
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import common
import numpy as np
import math

vartype = snakemake.wildcards.vartype
colors = common.get_colors(snakemake.config)

def props(callers):
    return product(callers, snakemake.params.len_ranges)

phred_to_log_factor = -0.23025850929940456
log_to_phred_factor = -4.3429448190325175

def plot_len_range(minlen, maxlen):
    for calls, (caller, len_range) in zip(snakemake.input.varlociraptor_calls, props(snakemake.params.varlociraptor_callers)):
        if len_range[0] != minlen and len_range[1] != maxlen:
            continue
        label = "varlociraptor+{}".format(caller)
        calls = pd.read_table(calls)
        calls["caller"] = label
        if not calls.empty:
            color = colors[caller]
            sns.kdeplot(calls[calls.is_tp].PROB_SOMATIC_TUMOR.map(np.log), color=color, label=label)
            sns.kdeplot(calls[~calls.is_tp].PROB_SOMATIC_TUMOR.map(np.log), color=color, linestyle=":", label="")

    ax = plt.gca()
    fmt_ticks = lambda ticks: ["{:.1g}".format(np.exp(t)) for t in ticks]
    ax.set_xticklabels(fmt_ticks(plt.xticks()[0]))
    ax.legend().remove()
    handles, _ = ax.get_legend_handles_labels()
    sns.despine()

    return ax, handles

common.plot_ranges(
    snakemake.params.len_ranges,
    plot_len_range,
    xlabel="Pr(somatic) (PHRED)",
    ylabel="density")

plt.savefig(snakemake.output[0], bbox_inches="tight")
plot_allelefreq_recall 2
  • plots/allelefreq-recall/simulated-bwa.INS.svg
  • plots/allelefreq-recall/simulated-bwa.DEL.svg
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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from itertools import product
import matplotlib
matplotlib.use("agg")
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import common
import numpy as np
import math
from matplotlib.lines import Line2D

MIN_CALLS = 10

vartype = snakemake.wildcards.vartype
colors = common.get_colors(snakemake.config)


def props(callers):
    return product(callers, snakemake.params.len_ranges)


def plot_len_range(minlen, maxlen):

    truth = common.load_variants(
        snakemake.input.truth, minlen, maxlen, vartype=vartype)

    afs = pd.Series(truth.TAF.unique()).sort_values()

    def plot(calls,
             label,
             color,
             varlociraptor=True,
             style="-.",
             markersize=4):
        calls = pd.read_table(calls, index_col=0)
        if len(calls) < 10:
            return
        if varlociraptor:
            phred = lambda p: -10 * math.log10(p)
            def calc_recall(p):
                c = calls[calls.score <= phred(p)]
                return [common.recall(c, truth[truth.TAF >= af]) for af in afs]

            return plt.fill_between(
                afs,
                calc_recall(0.98 if maxlen > 30 else 0.99),
                calc_recall(0.9),
                color=color,
                label=label,
                alpha=0.6)
        else:
            recall = [common.recall(calls, truth[truth.TAF >= af]) for af in afs]
            # plot a white background first to increase visibility
            plt.plot(afs, recall, "-", color="white", alpha=0.8)
            return plt.plot(
                afs,
                recall,
                style,
                color=color,
                label=label)[0]

    handles = []
    def register_handle(handle):
        if handle is not None:
            handles.append(handle)
    for calls, (caller,
                len_range) in zip(snakemake.input.varlociraptor_calls,
                                  props(snakemake.params.varlociraptor_callers)):
        if len_range[0] != minlen and len_range[1] != maxlen:
            continue
        label = "varlociraptor+{}".format(caller)
        handle = plot(calls, label, colors[caller], varlociraptor=True)
        register_handle(handle)
        #handles.append(Line2D([0], [0], color=colors[caller], label=label))

    for calls, (caller, len_range) in zip(snakemake.input.adhoc_calls,
                             props(snakemake.params.adhoc_callers)):
        if len_range[0] != minlen and len_range[1] != maxlen:
            continue
        color = colors[caller]
        handle = plot(calls, caller, color, style=":", varlociraptor=False)
        register_handle(handle)
        #handles.append(Line2D([0], [0], linestyle=":", color=color, label=caller))

    sns.despine()
    ax = plt.gca()
    return ax, handles


common.plot_ranges(
    snakemake.params.len_ranges,
    plot_len_range,
    xlabel="allele frequency",
    ylabel="recall")

plt.savefig(snakemake.output[0], bbox_inches="tight")
plot_allelefreq_scatter 2
  • plots/allelefreq-scatter/simulated-bwa.INS.svg
  • plots/allelefreq-scatter/simulated-bwa.DEL.svg
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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import math
import matplotlib
matplotlib.use("agg")
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import common
import numpy as np

MIN_COUNT = 20
MAX_DEPTH = 60

vartype = snakemake.wildcards.vartype
colors = common.get_colors(snakemake.config)

truth = common.load_variants(snakemake.input.truth, vartype=vartype)

all_calls = []
for caller, calls in zip(snakemake.params.callers, snakemake.input.calls):
    calls = pd.read_table(calls)
    calls.loc[:, "caller"] = caller
    all_calls.append(calls)
all_calls = pd.concat(all_calls)

def plot(af, _):
    constrain_lower = lambda error: np.maximum(error, -af)
    constrain_upper = lambda error: np.minimum(error, 1.0 - af)

    dp = all_calls["TUMOR_DP"]
    calls = all_calls[all_calls.is_tp]
    true_af = truth.loc[calls.MATCHING].reset_index().TAF
    calls = calls.reset_index()
    calls["true_af"] = true_af
    calls = calls[calls["true_af"] == af]
    calls["error"] = calls.CASE_AF - true_af

    sns.kdeplot(calls["TUMOR_DP"], calls["error"], cmap="Blues", n_levels=50, shade=True, alpha=0.7, shade_lowest=False) #alpha=0.5, clip=((0.0, 1.0), (0.0, af)))
    plt.plot(calls["TUMOR_DP"], calls["error"], ",", color="k", lw=0, alpha=1.0, rasterized=True)
    by_depth = calls.groupby("TUMOR_DP")["error"].describe().reset_index()
    by_depth["-std"] = constrain_lower(-by_depth["std"])
    by_depth["std"] = constrain_upper(by_depth["std"])
    by_depth = by_depth[by_depth["count"] >= MIN_COUNT]
    plt.plot(by_depth.TUMOR_DP, by_depth["std"], "--", color="k")
    plt.plot(by_depth.TUMOR_DP, by_depth["-std"], "--", color="k")
    plt.plot(by_depth.TUMOR_DP, by_depth["mean"], "-", color="k")

    depths = np.arange(0, MAX_DEPTH)
    # standard deviation when sampling in binomial process from allele freq
    # this is the expected sampling error within the correctly mapped fragments
    sd = np.array([1.0 / depth * math.sqrt(depth * af * (1.0 - af)) for depth in depths])
    plt.fill_between(depths, constrain_lower(-sd), constrain_upper(sd), color="grey", alpha=0.5)
    
    sns.despine()
    plt.xticks(rotation="vertical")
    ax = plt.gca()
    ax.legend().remove()
    handles, labels = ax.get_legend_handles_labels()
    plt.ylim((-1.0, 1.0))
    plt.xlim((0, MAX_DEPTH))

    return ax, []

afs = [(af, af) for af in truth.TAF.sort_values().unique()]

common.plot_ranges(
    afs,
    plot,
    "depth",
    "predicted - truth")

plt.savefig(snakemake.output[0], bbox_inches="tight")
plot_concordance 2
  • plots/concordance/colo1.INS.concordance.svg
  • plots/concordance/colo1.DEL.concordance.svg
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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from itertools import product
import matplotlib
matplotlib.use("agg")
from matplotlib import pyplot as plt
import seaborn as sns
import pandas as pd
import common
import numpy as np
import math
from matplotlib.lines import Line2D
from matplotlib.colors import to_rgba


class NotEnoughObservationsException(Exception):
    pass


MIN_CALLS = 20
MAX_LEN = 1000

vartype = snakemake.wildcards.vartype
colors = common.get_colors(snakemake.config)



varlociraptor_calls_low = [pd.read_table(f) for f in snakemake.input.varlociraptor_calls_low]
varlociraptor_calls_high = [pd.read_table(f) for f in snakemake.input.varlociraptor_calls_high]
adhoc_calls = [pd.read_table(f) for f in snakemake.input.adhoc_calls]


def expected_count(af, effective_mutation_rate):
    """Calculate the expected number of somatic variants
       greater than a given allele frequency given an effective mutation
       rate, according to the model of Williams et al. Nature 
       Genetics 2016"""
    return effective_mutation_rate * (1.0 / af - 1.0)


def expected_counts(afs, effective_mutation_rate):
    return [expected_count(af, effective_mutation_rate) for af in afs]


def calc_concordance(calls):
    n = len(calls)
    return (calls["concordance_count"] > 1).sum() / n


def plot_len_range(minlen, maxlen, yfunc=None, yscale=None, upper_bound=None):
    handles_varlociraptor = []
    handles_adhoc = []
    for i, caller in enumerate(snakemake.params.callers):
        def plot_calls(calls, label, color, style, calls_lower=None):
            def get_xy(calls, caseafs=None):
                svlen = calls.loc[:, calls.columns.str.startswith("SVLEN")].abs()
                # at least one of the calls has a valid svlen
                valid = ((svlen >= minlen) & (svlen <= maxlen)).sum(axis=1) >= 1
                calls = calls[valid]
                if caseafs is None:
                    caseafs = calls["max_case_af"].dropna().unique()
                y = []
                _caseafs = []
                for caseaf in sorted(caseafs):
                    _calls = calls[calls["max_case_af"] >= caseaf]
                    if upper_bound is not None:
                        _calls = _calls[_calls["max_case_af"] <= caseaf + upper_bound]
                    if len(_calls) < MIN_CALLS:
                        continue
                    _caseafs.append(caseaf)
                    y.append(yfunc(_calls))
                return _caseafs, y

            x, y = get_xy(calls)
            if not x:
                raise NotEnoughObservationsException()
            if calls_lower is not None:
                _, y2 = get_xy(calls_lower, caseafs=x)
                return plt.fill_between(x, y, y2, label=label, edgecolor=color, facecolor=to_rgba(color, alpha=0.2))
            else:
                if style != "-":
                    plt.plot(x, y, "-", color="white", alpha=0.8)
                return plt.plot(x, y, style, label=label, color=color)[0]

        color = colors[snakemake.params.callers[i]]
        try:
            handles_varlociraptor.append(
                plot_calls(
                    varlociraptor_calls_high[i], 
                    "varlociraptor+{}".format(caller), 
                    color=color, style="-", 
                    calls_lower=varlociraptor_calls_low[i]))
        except NotEnoughObservationsException:
            # skip plot
            pass
        try:
            handles_adhoc.append(plot_calls(adhoc_calls[i], caller, color=color, style=":"))
        except NotEnoughObservationsException:
            # skip plot
            pass

    handles = handles_varlociraptor + handles_adhoc
    sns.despine()
    ax = plt.gca()
    if yscale is not None:
        ax.set_yscale(yscale)
    return ax, handles

plt.figure(figsize=(10, 4))
plt.subplot(121)
plot_len_range(1, MAX_LEN, yfunc=calc_concordance)
plt.xlabel("$\geq$ tumor allele frequency")
plt.ylabel("concordance")

plt.subplot(122)
for effective_mutation_rate in 10 ** np.linspace(1, 5, 7):
    afs = np.linspace(0.0, 1.0, 100, endpoint=False)
    plt.semilogy(afs, expected_counts(afs, effective_mutation_rate), "-", color="grey", alpha=0.4)

ax, handles = plot_len_range(1, MAX_LEN, yfunc=lambda calls: len(calls), yscale="log")

plt.xlabel("$\geq$ tumor allele frequency")
plt.ylabel("# of calls")

ax.legend(handles=handles, loc="upper left", bbox_to_anchor=(1.0, 1.0))

plt.tight_layout()

plt.savefig(snakemake.output[0], bbox_inches="tight")
obtain_tp_fp 416
  • annotated-calls/varlociraptor-delly/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/varlociraptor-delly/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/default-lancet/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/default-lancet/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/default-manta/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/default-manta/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/default-strelka/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/default-strelka/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/adhoc-delly/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/adhoc-delly/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/adhoc-lancet/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/adhoc-lancet/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/adhoc-manta/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/adhoc-manta/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/adhoc-strelka/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/adhoc-strelka/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/adhoc-bpi/simulated-bwa.INS.1-30.1.0.tsv
  • annotated-calls/adhoc-bpi/simulated-bwa.INS.30-100.1.0.tsv
  • annotated-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.1.0.tsv
  • annotated-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.1.0.tsv
  • annotated-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.1.0.tsv
  • annotated-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.1.0.tsv
  • annotated-calls/default-lancet/simulated-bwa.DEL.1-30.1.0.tsv
  • annotated-calls/default-lancet/simulated-bwa.DEL.30-50.1.0.tsv
  • annotated-calls/default-lancet/simulated-bwa.DEL.50-100.1.0.tsv
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  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.1e-05.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.0001.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.001.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.01.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.05.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.1.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.2.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.3.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.4.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.5.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.6.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.7.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.8.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.9.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.1e-05.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.0001.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.001.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.01.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.05.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.1.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.2.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.3.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.4.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.5.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.6.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.7.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.8.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.9.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.1e-05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.0001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.01.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.1.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.2.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.3.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.4.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.5.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.6.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.7.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.8.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.9.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.1e-05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.0001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.01.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.1.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.2.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.3.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.4.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.5.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.6.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.7.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.8.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.9.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.1e-05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.0001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.01.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.1.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.2.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.3.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.4.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.5.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.6.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.7.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.8.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.9.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.1e-05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.0001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.001.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.01.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.05.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.1.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.2.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.3.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.4.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.5.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.6.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.7.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.8.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.9.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.1e-05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.0001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.01.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.1.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.2.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.3.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.4.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.5.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.6.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.7.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.8.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.9.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.1e-05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.0001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.01.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.1.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.2.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.3.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.4.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.5.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.6.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.7.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.8.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.9.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.1e-05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.0001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.01.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.1.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.2.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.3.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.4.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.5.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.6.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.7.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.8.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.9.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.1e-05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.0001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.001.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.01.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.05.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.1.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.2.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.3.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.4.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.5.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.6.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.7.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.8.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.9.tsv
  • annotated-calls/varlociraptor-delly/simulated-bwa.INS.1-250.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.INS.1-250.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.INS.1-250.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.INS.1-250.1.0.tsv
  • annotated-calls/varlociraptor-delly/simulated-bwa.DEL.1-250.1.0.tsv
  • annotated-calls/varlociraptor-lancet/simulated-bwa.DEL.1-250.1.0.tsv
  • annotated-calls/varlociraptor-manta/simulated-bwa.DEL.1-250.1.0.tsv
  • annotated-calls/varlociraptor-strelka/simulated-bwa.DEL.1-250.1.0.tsv
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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import pandas as pd
import numpy as np
from common import load_variants


minlen = int(snakemake.wildcards.minlen)
maxlen = int(snakemake.wildcards.maxlen)
vartype = snakemake.wildcards.vartype

if snakemake.wildcards.mode == "varlociraptor":
    score = snakemake.config["caller"]["varlociraptor"]["score"]
    # calls are already filtered by FDR control step
    minlen = None
    maxlen = None
elif snakemake.wildcards.mode == "default":
    score = snakemake.config["caller"][snakemake.wildcards.caller]["score"]
else:
    score = None

calls = load_variants(snakemake.input.calls, vartype=vartype, minlen=minlen, maxlen=maxlen)

calls["is_tp"] = calls["MATCHING"] >= 0

calls["score"] = calls[score] if score else np.nan

calls.to_csv(snakemake.output[0], sep="\t")
aggregate_concordance 30
  • aggregated-concordance/varlociraptor-delly-0.9/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-lancet-0.9/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-manta-0.9/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-strelka-0.9/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-bpi-0.9/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-delly-0.98/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-lancet-0.98/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-manta-0.98/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-strelka-0.98/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-bpi-0.98/colo1.INS.tsv
  • aggregated-concordance/adhoc-delly-default/colo1.INS.tsv
  • aggregated-concordance/adhoc-lancet-default/colo1.INS.tsv
  • aggregated-concordance/adhoc-manta-default/colo1.INS.tsv
  • aggregated-concordance/adhoc-strelka-default/colo1.INS.tsv
  • aggregated-concordance/adhoc-bpi-default/colo1.INS.tsv
  • aggregated-concordance/varlociraptor-delly-0.9/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-lancet-0.9/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-manta-0.9/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-strelka-0.9/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-bpi-0.9/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-delly-0.98/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-lancet-0.98/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-manta-0.98/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-strelka-0.98/colo1.DEL.tsv
  • aggregated-concordance/varlociraptor-bpi-0.98/colo1.DEL.tsv
  • aggregated-concordance/adhoc-delly-default/colo1.DEL.tsv
  • aggregated-concordance/adhoc-lancet-default/colo1.DEL.tsv
  • aggregated-concordance/adhoc-manta-default/colo1.DEL.tsv
  • aggregated-concordance/adhoc-strelka-default/colo1.DEL.tsv
  • aggregated-concordance/adhoc-bpi-default/colo1.DEL.tsv
  • python =3.6
  • pandas =0.23
  • matplotlib =3.0
  • seaborn =0.9.0
  • pysam =0.13.0
  • svgutils =0.2
  • pybedtools =0.7.10
  • networkx =2.2
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from common import load_variants
import networkx as nx
import pandas as pd
import numpy as np

vartype = snakemake.wildcards.vartype

index_cols = ["CHROM", "POS", "SVLEN"] if vartype == "INS" or vartype == "DEL" else ["CHROM", "POS", "ALT"]

all_variants = [load_variants(f, vartype=vartype) for f in snakemake.input.calls]

G = nx.Graph()
for calls, (i, j) in zip(all_variants, snakemake.params.dataset_combinations):
    calls["component"] = None
    for call in calls.itertuples():
        a = (i, call.Index)
        G.add_node(a)
        if call.MATCHING >= 0:
            b = (j, call.MATCHING)
            G.add_node(b)
            G.add_edge(a, b)

# get a set of calls for each dataset (we don't need all pairwise comparisons for that)
representatives = {snakemake.params.dataset_combinations[i][0]: calls for i, calls in enumerate(all_variants)}

if snakemake.wildcards.mode != "varlociraptor":
    varlociraptor_variants = [load_variants(f, vartype=vartype) for f in snakemake.input.varlociraptor_calls]
    for calls in varlociraptor_variants:
        calls.set_index(index_cols, inplace=True)
    varlociraptor_representatives = {snakemake.params.dataset_combinations[i][0]: calls for i, calls in enumerate(varlociraptor_variants)}

# annotate calls with their component, i.e. their equivalence class
for component_id, component in enumerate(nx.connected_components(G)):
    for i, k in component:
        representatives[i].loc[k, "component"] = component_id
for calls in representatives.values():
    calls["component"] = calls["component"].astype(np.float32)
    calls.set_index("component", inplace=True)

# join calls based on their equivalence class
aggregated = None
suffix = "_{}".format
dataset_name = lambda i: snakemake.params.datasets[i]
is_varlociraptor = False
for dataset_id, calls in representatives.items():
    cols = list(index_cols)
    if "CASE_AF" in calls.columns:
        cols.extend(["CASE_AF", "PROB_SOMATIC_TUMOR"])
        is_varlociraptor = True
    calls = calls[cols]
    if snakemake.wildcards.mode != "varlociraptor":
        caseaf = calls.set_index(cols, drop=False).join(varlociraptor_representatives[dataset_id][["CASE_AF"]], how="left")["CASE_AF"]
        caseaf = caseaf[~caseaf.index.duplicated()]
        calls["CASE_AF"] = caseaf.values

    calls.columns = [c + suffix(dataset_name(dataset_id)) for c in calls.columns]
    if aggregated is None:
        aggregated = calls
    else:
        aggregated = aggregated.join(calls, how="outer", lsuffix="", rsuffix="")

# Forget the component id. Otherwise, we might run into errors with duplicate elements
# in the index below. These can occur if there are multiple ambiguous calls.
aggregated.reset_index(inplace=True, drop=True)

pos_cols = aggregated.columns[aggregated.columns.str.startswith("POS_")]
is_called = (~aggregated[pos_cols].isnull()).astype(int)
is_called.columns = pos_cols.str.replace("POS_", "")
aggregated = aggregated.join(is_called, lsuffix="", rsuffix="")

aggregated.insert(len(aggregated.columns), "concordance_count", is_called.sum(axis=1))

aggregated["max_case_af"] = aggregated[aggregated.columns[aggregated.columns.str.startswith("CASE_AF")]].max(axis=1)
if is_varlociraptor:
    aggregated["max_prob_somatic_tumor"] =  aggregated[aggregated.columns[aggregated.columns.str.startswith("PROB_SOMATIC")]].min(axis=1)

aggregated.to_csv(snakemake.output[0], sep="\t", index=False)
varlociraptor_calls_to_tsv 368
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.1.0.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.1.0.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.1.0.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.1.0.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.1.0.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.1.0.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.1e-05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.0001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.01.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.1.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.2.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.3.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.4.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.5.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.6.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.7.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.8.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.9.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.1e-05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.0001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.01.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.1.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.2.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.3.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.4.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.5.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.6.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.7.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.8.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.9.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.1e-05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.0001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.01.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.1.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.2.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.3.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.4.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.5.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.6.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.7.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.8.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.9.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.1e-05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.0001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.01.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.1.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.2.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.3.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.4.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.5.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.6.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.7.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.8.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.9.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.1e-05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.0001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.01.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.1.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.2.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.3.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.4.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.5.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.6.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.7.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.8.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.9.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.1e-05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.0001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.01.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.1.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.2.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.3.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.4.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.5.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.6.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.7.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.8.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.9.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.1e-05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.0001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.01.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.1.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.2.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.3.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.4.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.5.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.6.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.7.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.8.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.9.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.1e-05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.0001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.01.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.1.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.2.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.3.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.4.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.5.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.6.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.7.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.8.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.9.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.1e-05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.0001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.01.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.1.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.2.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.3.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.4.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.5.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.6.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.7.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.8.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.9.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.1e-05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.0001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.01.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.1.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.2.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.3.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.4.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.5.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.6.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.7.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.8.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.9.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.1e-05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.0001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.01.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.1.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.2.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.3.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.4.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.5.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.6.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.7.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.8.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.9.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.1e-05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.0001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.001.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.01.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.05.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.1.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.2.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.3.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.4.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.5.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.6.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.7.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.8.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.9.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.1e-05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.0001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.01.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.1.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.2.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.3.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.4.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.5.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.6.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.7.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.8.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.9.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.1e-05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.0001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.01.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.1.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.2.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.3.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.4.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.5.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.6.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.7.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.8.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.9.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.1e-05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.0001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.01.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.1.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.2.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.3.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.4.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.5.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.6.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.7.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.8.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.9.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.1e-05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.0001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.001.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.01.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.05.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.1.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.2.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.3.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.4.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.5.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.6.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.7.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.8.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.9.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.1e-05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.0001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.01.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.1.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.2.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.3.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.4.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.5.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.6.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.7.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.8.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.9.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.1e-05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.0001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.01.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.1.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.2.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.3.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.4.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.5.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.6.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.7.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.8.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.9.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.1e-05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.0001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.01.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.1.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.2.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.3.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.4.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.5.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.6.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.7.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.8.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.9.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.1e-05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.0001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.001.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.01.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.05.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.1.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.2.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.3.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.4.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.5.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.6.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.7.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.8.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.9.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.1e-05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.0001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.01.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.1.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.2.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.3.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.4.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.5.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.6.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.7.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.8.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.9.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.1e-05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.0001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.01.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.1.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.2.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.3.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.4.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.5.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.6.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.7.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.8.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.9.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.1e-05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.0001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.01.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.1.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.2.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.3.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.4.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.5.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.6.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.7.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.8.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.9.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.1e-05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.0001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.001.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.01.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.05.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.1.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.2.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.3.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.4.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.5.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.6.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.7.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.8.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.9.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-250.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-250.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-250.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-250.1.0.tsv
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-250.1.0.tsv
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-250.1.0.tsv
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-250.1.0.tsv
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-250.1.0.tsv
  • rust-bio-tools =0.5.0
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-to-txt {params.gt} {params.tags} --info MATCHING < {input} > {output}
other_calls_to_tsv 8
  • matched-calls/default-lancet/simulated-bwa.all.tsv
  • matched-calls/default-manta/simulated-bwa.all.tsv
  • matched-calls/default-strelka/simulated-bwa.all.tsv
  • matched-calls/adhoc-delly/simulated-bwa.all.tsv
  • matched-calls/adhoc-lancet/simulated-bwa.all.tsv
  • matched-calls/adhoc-manta/simulated-bwa.all.tsv
  • matched-calls/adhoc-strelka/simulated-bwa.all.tsv
  • matched-calls/adhoc-bpi/simulated-bwa.all.tsv
  • rust-bio-tools =0.2.5
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-to-txt {params.gt} {params.tags} --info MATCHING < {input} > {output}
concordance_to_tsv 60
  • concordance/varlociraptor-delly-0.9/colo1.0-vs-1.tsv
  • concordance/varlociraptor-delly-0.9/colo1.1-vs-2.tsv
  • concordance/varlociraptor-delly-0.9/colo1.2-vs-0.tsv
  • concordance/varlociraptor-delly-0.9/colo1.2-vs-3.tsv
  • concordance/varlociraptor-delly-0.9/colo1.3-vs-0.tsv
  • concordance/varlociraptor-delly-0.9/colo1.3-vs-1.tsv
  • concordance/varlociraptor-lancet-0.9/colo1.0-vs-1.tsv
  • concordance/varlociraptor-lancet-0.9/colo1.1-vs-2.tsv
  • concordance/varlociraptor-lancet-0.9/colo1.2-vs-0.tsv
  • concordance/varlociraptor-lancet-0.9/colo1.2-vs-3.tsv
  • concordance/varlociraptor-lancet-0.9/colo1.3-vs-0.tsv
  • concordance/varlociraptor-lancet-0.9/colo1.3-vs-1.tsv
  • concordance/varlociraptor-manta-0.9/colo1.0-vs-1.tsv
  • concordance/varlociraptor-manta-0.9/colo1.1-vs-2.tsv
  • concordance/varlociraptor-manta-0.9/colo1.2-vs-0.tsv
  • concordance/varlociraptor-manta-0.9/colo1.2-vs-3.tsv
  • concordance/varlociraptor-manta-0.9/colo1.3-vs-0.tsv
  • concordance/varlociraptor-manta-0.9/colo1.3-vs-1.tsv
  • concordance/varlociraptor-strelka-0.9/colo1.0-vs-1.tsv
  • concordance/varlociraptor-strelka-0.9/colo1.1-vs-2.tsv
  • concordance/varlociraptor-strelka-0.9/colo1.2-vs-0.tsv
  • concordance/varlociraptor-strelka-0.9/colo1.2-vs-3.tsv
  • concordance/varlociraptor-strelka-0.9/colo1.3-vs-0.tsv
  • concordance/varlociraptor-strelka-0.9/colo1.3-vs-1.tsv
  • concordance/varlociraptor-bpi-0.9/colo1.0-vs-1.tsv
  • concordance/varlociraptor-bpi-0.9/colo1.1-vs-2.tsv
  • concordance/varlociraptor-bpi-0.9/colo1.2-vs-0.tsv
  • concordance/varlociraptor-bpi-0.9/colo1.2-vs-3.tsv
  • concordance/varlociraptor-bpi-0.9/colo1.3-vs-0.tsv
  • concordance/varlociraptor-bpi-0.9/colo1.3-vs-1.tsv
  • concordance/varlociraptor-delly-0.98/colo1.0-vs-1.tsv
  • concordance/varlociraptor-delly-0.98/colo1.1-vs-2.tsv
  • concordance/varlociraptor-delly-0.98/colo1.2-vs-0.tsv
  • concordance/varlociraptor-delly-0.98/colo1.2-vs-3.tsv
  • concordance/varlociraptor-delly-0.98/colo1.3-vs-0.tsv
  • concordance/varlociraptor-delly-0.98/colo1.3-vs-1.tsv
  • concordance/varlociraptor-lancet-0.98/colo1.0-vs-1.tsv
  • concordance/varlociraptor-lancet-0.98/colo1.1-vs-2.tsv
  • concordance/varlociraptor-lancet-0.98/colo1.2-vs-0.tsv
  • concordance/varlociraptor-lancet-0.98/colo1.2-vs-3.tsv
  • concordance/varlociraptor-lancet-0.98/colo1.3-vs-0.tsv
  • concordance/varlociraptor-lancet-0.98/colo1.3-vs-1.tsv
  • concordance/varlociraptor-manta-0.98/colo1.0-vs-1.tsv
  • concordance/varlociraptor-manta-0.98/colo1.1-vs-2.tsv
  • concordance/varlociraptor-manta-0.98/colo1.2-vs-0.tsv
  • concordance/varlociraptor-manta-0.98/colo1.2-vs-3.tsv
  • concordance/varlociraptor-manta-0.98/colo1.3-vs-0.tsv
  • concordance/varlociraptor-manta-0.98/colo1.3-vs-1.tsv
  • concordance/varlociraptor-strelka-0.98/colo1.0-vs-1.tsv
  • concordance/varlociraptor-strelka-0.98/colo1.1-vs-2.tsv
  • concordance/varlociraptor-strelka-0.98/colo1.2-vs-0.tsv
  • concordance/varlociraptor-strelka-0.98/colo1.2-vs-3.tsv
  • concordance/varlociraptor-strelka-0.98/colo1.3-vs-0.tsv
  • concordance/varlociraptor-strelka-0.98/colo1.3-vs-1.tsv
  • concordance/varlociraptor-bpi-0.98/colo1.0-vs-1.tsv
  • concordance/varlociraptor-bpi-0.98/colo1.1-vs-2.tsv
  • concordance/varlociraptor-bpi-0.98/colo1.2-vs-0.tsv
  • concordance/varlociraptor-bpi-0.98/colo1.2-vs-3.tsv
  • concordance/varlociraptor-bpi-0.98/colo1.3-vs-0.tsv
  • concordance/varlociraptor-bpi-0.98/colo1.3-vs-1.tsv
  • rust-bio-tools =0.5.0
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-to-txt {params.gt} {params.tags} --info MATCHING < {input} > {output}
concordance_to_tsv 30
  • concordance/adhoc-delly-default/colo1.0-vs-1.tsv
  • concordance/adhoc-delly-default/colo1.1-vs-2.tsv
  • concordance/adhoc-delly-default/colo1.2-vs-0.tsv
  • concordance/adhoc-delly-default/colo1.2-vs-3.tsv
  • concordance/adhoc-delly-default/colo1.3-vs-0.tsv
  • concordance/adhoc-delly-default/colo1.3-vs-1.tsv
  • concordance/adhoc-lancet-default/colo1.0-vs-1.tsv
  • concordance/adhoc-lancet-default/colo1.1-vs-2.tsv
  • concordance/adhoc-lancet-default/colo1.2-vs-0.tsv
  • concordance/adhoc-lancet-default/colo1.2-vs-3.tsv
  • concordance/adhoc-lancet-default/colo1.3-vs-0.tsv
  • concordance/adhoc-lancet-default/colo1.3-vs-1.tsv
  • concordance/adhoc-manta-default/colo1.0-vs-1.tsv
  • concordance/adhoc-manta-default/colo1.1-vs-2.tsv
  • concordance/adhoc-manta-default/colo1.2-vs-0.tsv
  • concordance/adhoc-manta-default/colo1.2-vs-3.tsv
  • concordance/adhoc-manta-default/colo1.3-vs-0.tsv
  • concordance/adhoc-manta-default/colo1.3-vs-1.tsv
  • concordance/adhoc-strelka-default/colo1.0-vs-1.tsv
  • concordance/adhoc-strelka-default/colo1.1-vs-2.tsv
  • concordance/adhoc-strelka-default/colo1.2-vs-0.tsv
  • concordance/adhoc-strelka-default/colo1.2-vs-3.tsv
  • concordance/adhoc-strelka-default/colo1.3-vs-0.tsv
  • concordance/adhoc-strelka-default/colo1.3-vs-1.tsv
  • concordance/adhoc-bpi-default/colo1.0-vs-1.tsv
  • concordance/adhoc-bpi-default/colo1.1-vs-2.tsv
  • concordance/adhoc-bpi-default/colo1.2-vs-0.tsv
  • concordance/adhoc-bpi-default/colo1.2-vs-3.tsv
  • concordance/adhoc-bpi-default/colo1.3-vs-0.tsv
  • concordance/adhoc-bpi-default/colo1.3-vs-1.tsv
  • rust-bio-tools =0.2.5
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-to-txt {params.gt} {params.tags} --info MATCHING < {input} > {output}
varlociraptor_all_calls_to_tsv 20
  • varlociraptor-delly/COLO_829-GSC.all.tsv
  • varlociraptor-delly/COLO_829-Ill.all.tsv
  • varlociraptor-delly/COLO_829-TGen.all.tsv
  • varlociraptor-delly/COLO_829-EBI.all.tsv
  • varlociraptor-lancet/COLO_829-GSC.all.tsv
  • varlociraptor-lancet/COLO_829-Ill.all.tsv
  • varlociraptor-lancet/COLO_829-TGen.all.tsv
  • varlociraptor-lancet/COLO_829-EBI.all.tsv
  • varlociraptor-manta/COLO_829-GSC.all.tsv
  • varlociraptor-manta/COLO_829-Ill.all.tsv
  • varlociraptor-manta/COLO_829-TGen.all.tsv
  • varlociraptor-manta/COLO_829-EBI.all.tsv
  • varlociraptor-strelka/COLO_829-GSC.all.tsv
  • varlociraptor-strelka/COLO_829-Ill.all.tsv
  • varlociraptor-strelka/COLO_829-TGen.all.tsv
  • varlociraptor-strelka/COLO_829-EBI.all.tsv
  • varlociraptor-bpi/COLO_829-GSC.all.tsv
  • varlociraptor-bpi/COLO_829-Ill.all.tsv
  • varlociraptor-bpi/COLO_829-TGen.all.tsv
  • varlociraptor-bpi/COLO_829-EBI.all.tsv
  • rust-bio-tools =0.5.0
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-to-txt {params.gt} {params.tags} < {input} > {output}
match_varlociraptor_calls 368
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.1.0.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.1.0.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.1.0.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.1.0.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.1.0.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.1.0.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.1e-05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.0001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.01.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.1.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.2.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.3.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.4.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.5.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.6.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.7.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.8.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-30.0.9.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.1e-05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.0001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.01.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.1.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.2.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.3.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.4.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.5.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.6.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.7.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.8.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.30-100.0.9.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.1e-05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.0001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.01.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.1.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.2.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.3.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.4.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.5.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.6.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.7.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.8.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-30.0.9.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.1e-05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.0001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.01.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.1.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.2.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.3.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.4.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.5.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.6.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.7.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.8.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.30-100.0.9.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.1e-05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.0001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.01.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.1.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.2.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.3.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.4.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.5.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.6.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.7.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.8.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-30.0.9.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.1e-05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.0001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.01.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.1.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.2.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.3.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.4.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.5.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.6.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.7.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.8.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.30-100.0.9.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.1e-05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.0001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.01.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.1.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.2.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.3.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.4.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.5.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.6.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.7.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.8.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-30.0.9.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.1e-05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.0001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.01.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.1.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.2.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.3.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.4.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.5.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.6.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.7.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.8.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.30-100.0.9.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.1e-05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.0001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.01.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.1.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.2.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.3.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.4.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.5.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.6.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.7.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.8.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-30.0.9.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.1e-05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.0001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.01.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.1.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.2.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.3.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.4.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.5.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.6.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.7.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.8.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.30-50.0.9.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.1e-05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.0001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.01.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.1.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.2.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.3.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.4.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.5.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.6.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.7.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.8.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.50-100.0.9.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.1e-05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.0001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.001.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.01.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.05.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.1.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.2.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.3.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.4.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.5.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.6.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.7.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.8.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.100-250.0.9.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.1e-05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.0001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.01.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.1.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.2.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.3.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.4.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.5.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.6.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.7.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.8.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-30.0.9.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.1e-05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.0001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.01.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.1.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.2.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.3.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.4.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.5.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.6.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.7.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.8.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.30-50.0.9.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.1e-05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.0001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.01.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.1.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.2.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.3.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.4.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.5.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.6.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.7.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.8.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.50-100.0.9.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.1e-05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.0001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.001.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.01.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.05.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.1.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.2.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.3.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.4.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.5.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.6.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.7.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.8.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.100-250.0.9.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.1e-05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.0001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.01.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.1.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.2.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.3.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.4.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.5.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.6.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.7.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.8.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-30.0.9.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.1e-05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.0001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.01.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.1.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.2.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.3.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.4.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.5.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.6.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.7.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.8.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.30-50.0.9.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.1e-05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.0001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.01.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.1.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.2.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.3.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.4.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.5.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.6.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.7.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.8.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.50-100.0.9.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.1e-05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.0001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.001.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.01.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.05.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.1.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.2.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.3.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.4.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.5.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.6.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.7.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.8.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.100-250.0.9.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.1e-05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.0001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.01.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.1.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.2.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.3.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.4.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.5.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.6.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.7.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.8.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-30.0.9.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.1e-05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.0001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.01.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.1.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.2.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.3.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.4.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.5.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.6.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.7.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.8.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.30-50.0.9.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.1e-05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.0001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.01.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.1.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.2.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.3.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.4.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.5.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.6.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.7.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.8.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.50-100.0.9.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.1e-05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.0001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.001.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.01.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.05.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.1.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.2.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.3.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.4.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.5.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.6.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.7.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.8.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.100-250.0.9.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.INS.1-250.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.INS.1-250.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.INS.1-250.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.INS.1-250.1.0.bcf
  • matched-calls/varlociraptor-delly/simulated-bwa.DEL.1-250.1.0.bcf
  • matched-calls/varlociraptor-lancet/simulated-bwa.DEL.1-250.1.0.bcf
  • matched-calls/varlociraptor-manta/simulated-bwa.DEL.1-250.1.0.bcf
  • matched-calls/varlociraptor-strelka/simulated-bwa.DEL.1-250.1.0.bcf
  • rust-bio-tools =0.5.0
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-match {params} {input.truth} < {input.calls} > {output}
match_other_calls 8
  • matched-calls/default-lancet/simulated-bwa.all.bcf
  • matched-calls/default-manta/simulated-bwa.all.bcf
  • matched-calls/default-strelka/simulated-bwa.all.bcf
  • matched-calls/adhoc-delly/simulated-bwa.all.bcf
  • matched-calls/adhoc-lancet/simulated-bwa.all.bcf
  • matched-calls/adhoc-manta/simulated-bwa.all.bcf
  • matched-calls/adhoc-strelka/simulated-bwa.all.bcf
  • matched-calls/adhoc-bpi/simulated-bwa.all.bcf
1
rbt vcf-match {params} {input.truth} < {input.calls} > {output}
concordance_match 60
  • concordance/varlociraptor-delly-0.9/colo1.0-vs-1.bcf
  • concordance/varlociraptor-delly-0.9/colo1.1-vs-2.bcf
  • concordance/varlociraptor-delly-0.9/colo1.2-vs-0.bcf
  • concordance/varlociraptor-delly-0.9/colo1.2-vs-3.bcf
  • concordance/varlociraptor-delly-0.9/colo1.3-vs-0.bcf
  • concordance/varlociraptor-delly-0.9/colo1.3-vs-1.bcf
  • concordance/varlociraptor-lancet-0.9/colo1.0-vs-1.bcf
  • concordance/varlociraptor-lancet-0.9/colo1.1-vs-2.bcf
  • concordance/varlociraptor-lancet-0.9/colo1.2-vs-0.bcf
  • concordance/varlociraptor-lancet-0.9/colo1.2-vs-3.bcf
  • concordance/varlociraptor-lancet-0.9/colo1.3-vs-0.bcf
  • concordance/varlociraptor-lancet-0.9/colo1.3-vs-1.bcf
  • concordance/varlociraptor-manta-0.9/colo1.0-vs-1.bcf
  • concordance/varlociraptor-manta-0.9/colo1.1-vs-2.bcf
  • concordance/varlociraptor-manta-0.9/colo1.2-vs-0.bcf
  • concordance/varlociraptor-manta-0.9/colo1.2-vs-3.bcf
  • concordance/varlociraptor-manta-0.9/colo1.3-vs-0.bcf
  • concordance/varlociraptor-manta-0.9/colo1.3-vs-1.bcf
  • concordance/varlociraptor-strelka-0.9/colo1.0-vs-1.bcf
  • concordance/varlociraptor-strelka-0.9/colo1.1-vs-2.bcf
  • concordance/varlociraptor-strelka-0.9/colo1.2-vs-0.bcf
  • concordance/varlociraptor-strelka-0.9/colo1.2-vs-3.bcf
  • concordance/varlociraptor-strelka-0.9/colo1.3-vs-0.bcf
  • concordance/varlociraptor-strelka-0.9/colo1.3-vs-1.bcf
  • concordance/varlociraptor-bpi-0.9/colo1.0-vs-1.bcf
  • concordance/varlociraptor-bpi-0.9/colo1.1-vs-2.bcf
  • concordance/varlociraptor-bpi-0.9/colo1.2-vs-0.bcf
  • concordance/varlociraptor-bpi-0.9/colo1.2-vs-3.bcf
  • concordance/varlociraptor-bpi-0.9/colo1.3-vs-0.bcf
  • concordance/varlociraptor-bpi-0.9/colo1.3-vs-1.bcf
  • concordance/varlociraptor-delly-0.98/colo1.0-vs-1.bcf
  • concordance/varlociraptor-delly-0.98/colo1.1-vs-2.bcf
  • concordance/varlociraptor-delly-0.98/colo1.2-vs-0.bcf
  • concordance/varlociraptor-delly-0.98/colo1.2-vs-3.bcf
  • concordance/varlociraptor-delly-0.98/colo1.3-vs-0.bcf
  • concordance/varlociraptor-delly-0.98/colo1.3-vs-1.bcf
  • concordance/varlociraptor-lancet-0.98/colo1.0-vs-1.bcf
  • concordance/varlociraptor-lancet-0.98/colo1.1-vs-2.bcf
  • concordance/varlociraptor-lancet-0.98/colo1.2-vs-0.bcf
  • concordance/varlociraptor-lancet-0.98/colo1.2-vs-3.bcf
  • concordance/varlociraptor-lancet-0.98/colo1.3-vs-0.bcf
  • concordance/varlociraptor-lancet-0.98/colo1.3-vs-1.bcf
  • concordance/varlociraptor-manta-0.98/colo1.0-vs-1.bcf
  • concordance/varlociraptor-manta-0.98/colo1.1-vs-2.bcf
  • concordance/varlociraptor-manta-0.98/colo1.2-vs-0.bcf
  • concordance/varlociraptor-manta-0.98/colo1.2-vs-3.bcf
  • concordance/varlociraptor-manta-0.98/colo1.3-vs-0.bcf
  • concordance/varlociraptor-manta-0.98/colo1.3-vs-1.bcf
  • concordance/varlociraptor-strelka-0.98/colo1.0-vs-1.bcf
  • concordance/varlociraptor-strelka-0.98/colo1.1-vs-2.bcf
  • concordance/varlociraptor-strelka-0.98/colo1.2-vs-0.bcf
  • concordance/varlociraptor-strelka-0.98/colo1.2-vs-3.bcf
  • concordance/varlociraptor-strelka-0.98/colo1.3-vs-0.bcf
  • concordance/varlociraptor-strelka-0.98/colo1.3-vs-1.bcf
  • concordance/varlociraptor-bpi-0.98/colo1.0-vs-1.bcf
  • concordance/varlociraptor-bpi-0.98/colo1.1-vs-2.bcf
  • concordance/varlociraptor-bpi-0.98/colo1.2-vs-0.bcf
  • concordance/varlociraptor-bpi-0.98/colo1.2-vs-3.bcf
  • concordance/varlociraptor-bpi-0.98/colo1.3-vs-0.bcf
  • concordance/varlociraptor-bpi-0.98/colo1.3-vs-1.bcf
  • rust-bio-tools =0.5.0
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-match {params.match} {params.bcfs[1]} < {params.bcfs[0]} > {output}
concordance_match 30
  • concordance/adhoc-delly-default/colo1.0-vs-1.bcf
  • concordance/adhoc-delly-default/colo1.1-vs-2.bcf
  • concordance/adhoc-delly-default/colo1.2-vs-0.bcf
  • concordance/adhoc-delly-default/colo1.2-vs-3.bcf
  • concordance/adhoc-delly-default/colo1.3-vs-0.bcf
  • concordance/adhoc-delly-default/colo1.3-vs-1.bcf
  • concordance/adhoc-lancet-default/colo1.0-vs-1.bcf
  • concordance/adhoc-lancet-default/colo1.1-vs-2.bcf
  • concordance/adhoc-lancet-default/colo1.2-vs-0.bcf
  • concordance/adhoc-lancet-default/colo1.2-vs-3.bcf
  • concordance/adhoc-lancet-default/colo1.3-vs-0.bcf
  • concordance/adhoc-lancet-default/colo1.3-vs-1.bcf
  • concordance/adhoc-manta-default/colo1.0-vs-1.bcf
  • concordance/adhoc-manta-default/colo1.1-vs-2.bcf
  • concordance/adhoc-manta-default/colo1.2-vs-0.bcf
  • concordance/adhoc-manta-default/colo1.2-vs-3.bcf
  • concordance/adhoc-manta-default/colo1.3-vs-0.bcf
  • concordance/adhoc-manta-default/colo1.3-vs-1.bcf
  • concordance/adhoc-strelka-default/colo1.0-vs-1.bcf
  • concordance/adhoc-strelka-default/colo1.1-vs-2.bcf
  • concordance/adhoc-strelka-default/colo1.2-vs-0.bcf
  • concordance/adhoc-strelka-default/colo1.2-vs-3.bcf
  • concordance/adhoc-strelka-default/colo1.3-vs-0.bcf
  • concordance/adhoc-strelka-default/colo1.3-vs-1.bcf
  • concordance/adhoc-bpi-default/colo1.0-vs-1.bcf
  • concordance/adhoc-bpi-default/colo1.1-vs-2.bcf
  • concordance/adhoc-bpi-default/colo1.2-vs-0.bcf
  • concordance/adhoc-bpi-default/colo1.2-vs-3.bcf
  • concordance/adhoc-bpi-default/colo1.3-vs-0.bcf
  • concordance/adhoc-bpi-default/colo1.3-vs-1.bcf
  • rust-bio-tools =0.2.5
  • bedtools =2.27.1
  • bcftools =1.8
1
rbt vcf-match {params.match} {params.bcfs[1]} < {params.bcfs[0]} > {output}
varlociraptor_merge 24
  • varlociraptor-delly/COLO_829-GSC.all.bcf
  • varlociraptor-delly/COLO_829-Ill.all.bcf
  • varlociraptor-delly/COLO_829-TGen.all.bcf
  • varlociraptor-delly/COLO_829-EBI.all.bcf
  • varlociraptor-lancet/COLO_829-GSC.all.bcf
  • varlociraptor-lancet/COLO_829-Ill.all.bcf
  • varlociraptor-lancet/COLO_829-TGen.all.bcf
  • varlociraptor-lancet/COLO_829-EBI.all.bcf
  • varlociraptor-manta/COLO_829-GSC.all.bcf
  • varlociraptor-manta/COLO_829-Ill.all.bcf
  • varlociraptor-manta/COLO_829-TGen.all.bcf
  • varlociraptor-manta/COLO_829-EBI.all.bcf
  • varlociraptor-strelka/COLO_829-GSC.all.bcf
  • varlociraptor-strelka/COLO_829-Ill.all.bcf
  • varlociraptor-strelka/COLO_829-TGen.all.bcf
  • varlociraptor-strelka/COLO_829-EBI.all.bcf
  • varlociraptor-bpi/COLO_829-GSC.all.bcf
  • varlociraptor-bpi/COLO_829-Ill.all.bcf
  • varlociraptor-bpi/COLO_829-TGen.all.bcf
  • varlociraptor-bpi/COLO_829-EBI.all.bcf
  • varlociraptor-delly/simulated-bwa.all.bcf
  • varlociraptor-lancet/simulated-bwa.all.bcf
  • varlociraptor-manta/simulated-bwa.all.bcf
  • varlociraptor-strelka/simulated-bwa.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools concat {snakemake.params} -o {snakemake.output[0]} "
    "{snakemake.input}")
varlociraptor_control_fdr 368
  • varlociraptor-delly/simulated-bwa.INS.1-30.1.0.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.1.0.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.1.0.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.1.0.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.1.0.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.1.0.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.1.0.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.1.0.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.1.0.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.1.0.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.1.0.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.1.0.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.1e-05.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.0001.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.001.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.01.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.05.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.1.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.2.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.3.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.4.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.5.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.6.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.7.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.8.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-30.0.9.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.1e-05.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.0001.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.001.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.01.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.05.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.1.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.2.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.3.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.4.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.5.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.6.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.7.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.8.bcf
  • varlociraptor-delly/simulated-bwa.INS.30-100.0.9.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.1e-05.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.0001.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.001.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.01.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.05.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.1.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.2.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.3.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.4.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.5.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.6.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.7.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.8.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-30.0.9.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.1e-05.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.0001.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.001.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.01.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.05.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.1.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.2.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.3.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.4.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.5.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.6.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.7.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.8.bcf
  • varlociraptor-lancet/simulated-bwa.INS.30-100.0.9.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.1e-05.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.0001.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.001.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.01.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.05.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.1.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.2.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.3.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.4.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.5.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.6.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.7.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.8.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-30.0.9.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.1e-05.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.0001.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.001.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.01.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.05.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.1.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.2.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.3.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.4.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.5.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.6.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.7.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.8.bcf
  • varlociraptor-manta/simulated-bwa.INS.30-100.0.9.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.1e-05.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.0001.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.001.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.01.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.05.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.1.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.2.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.3.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.4.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.5.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.6.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.7.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.8.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-30.0.9.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.1e-05.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.0001.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.001.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.01.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.05.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.1.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.2.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.3.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.4.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.5.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.6.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.7.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.8.bcf
  • varlociraptor-strelka/simulated-bwa.INS.30-100.0.9.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.1e-05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.0001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.01.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.1.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.2.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.3.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.4.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.5.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.6.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.7.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.8.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-30.0.9.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.1e-05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.0001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.01.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.1.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.2.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.3.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.4.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.5.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.6.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.7.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.8.bcf
  • varlociraptor-delly/simulated-bwa.DEL.30-50.0.9.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.1e-05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.0001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.01.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.1.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.2.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.3.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.4.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.5.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.6.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.7.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.8.bcf
  • varlociraptor-delly/simulated-bwa.DEL.50-100.0.9.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.1e-05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.0001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.001.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.01.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.05.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.1.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.2.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.3.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.4.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.5.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.6.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.7.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.8.bcf
  • varlociraptor-delly/simulated-bwa.DEL.100-250.0.9.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.1e-05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.0001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.01.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.1.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.2.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.3.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.4.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.5.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.6.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.7.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.8.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-30.0.9.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.1e-05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.0001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.01.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.1.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.2.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.3.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.4.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.5.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.6.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.7.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.8.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.30-50.0.9.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.1e-05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.0001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.01.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.1.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.2.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.3.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.4.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.5.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.6.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.7.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.8.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.50-100.0.9.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.1e-05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.0001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.001.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.01.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.05.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.1.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.2.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.3.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.4.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.5.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.6.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.7.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.8.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.100-250.0.9.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.1e-05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.0001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.01.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.1.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.2.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.3.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.4.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.5.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.6.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.7.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.8.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-30.0.9.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.1e-05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.0001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.01.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.1.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.2.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.3.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.4.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.5.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.6.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.7.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.8.bcf
  • varlociraptor-manta/simulated-bwa.DEL.30-50.0.9.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.1e-05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.0001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.01.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.1.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.2.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.3.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.4.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.5.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.6.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.7.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.8.bcf
  • varlociraptor-manta/simulated-bwa.DEL.50-100.0.9.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.1e-05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.0001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.001.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.01.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.05.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.1.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.2.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.3.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.4.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.5.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.6.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.7.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.8.bcf
  • varlociraptor-manta/simulated-bwa.DEL.100-250.0.9.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.1e-05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.0001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.01.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.1.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.2.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.3.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.4.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.5.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.6.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.7.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.8.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-30.0.9.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.1e-05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.0001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.01.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.1.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.2.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.3.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.4.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.5.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.6.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.7.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.8.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.30-50.0.9.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.1e-05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.0001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.01.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.1.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.2.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.3.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.4.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.5.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.6.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.7.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.8.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.50-100.0.9.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.1e-05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.0001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.001.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.01.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.05.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.1.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.2.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.3.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.4.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.5.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.6.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.7.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.8.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.100-250.0.9.bcf
  • varlociraptor-delly/simulated-bwa.INS.1-250.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.INS.1-250.1.0.bcf
  • varlociraptor-manta/simulated-bwa.INS.1-250.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.INS.1-250.1.0.bcf
  • varlociraptor-delly/simulated-bwa.DEL.1-250.1.0.bcf
  • varlociraptor-lancet/simulated-bwa.DEL.1-250.1.0.bcf
  • varlociraptor-manta/simulated-bwa.DEL.1-250.1.0.bcf
  • varlociraptor-strelka/simulated-bwa.DEL.1-250.1.0.bcf
1
varlociraptor filter-calls control-fdr {input} --events SOMATIC_TUMOR --var {wildcards.type} --minlen {wildcards.minlen} --maxlen {wildcards.maxlen} --fdr {wildcards.fdr} > {output}
adhoc_varlociraptor 40
  • varlociraptor-delly/COLO_829-GSC.adhoc.0.9.bcf
  • varlociraptor-delly/COLO_829-Ill.adhoc.0.9.bcf
  • varlociraptor-delly/COLO_829-TGen.adhoc.0.9.bcf
  • varlociraptor-delly/COLO_829-EBI.adhoc.0.9.bcf
  • varlociraptor-lancet/COLO_829-GSC.adhoc.0.9.bcf
  • varlociraptor-lancet/COLO_829-Ill.adhoc.0.9.bcf
  • varlociraptor-lancet/COLO_829-TGen.adhoc.0.9.bcf
  • varlociraptor-lancet/COLO_829-EBI.adhoc.0.9.bcf
  • varlociraptor-manta/COLO_829-GSC.adhoc.0.9.bcf
  • varlociraptor-manta/COLO_829-Ill.adhoc.0.9.bcf
  • varlociraptor-manta/COLO_829-TGen.adhoc.0.9.bcf
  • varlociraptor-manta/COLO_829-EBI.adhoc.0.9.bcf
  • varlociraptor-strelka/COLO_829-GSC.adhoc.0.9.bcf
  • varlociraptor-strelka/COLO_829-Ill.adhoc.0.9.bcf
  • varlociraptor-strelka/COLO_829-TGen.adhoc.0.9.bcf
  • varlociraptor-strelka/COLO_829-EBI.adhoc.0.9.bcf
  • varlociraptor-bpi/COLO_829-GSC.adhoc.0.9.bcf
  • varlociraptor-bpi/COLO_829-Ill.adhoc.0.9.bcf
  • varlociraptor-bpi/COLO_829-TGen.adhoc.0.9.bcf
  • varlociraptor-bpi/COLO_829-EBI.adhoc.0.9.bcf
  • varlociraptor-delly/COLO_829-GSC.adhoc.0.98.bcf
  • varlociraptor-delly/COLO_829-Ill.adhoc.0.98.bcf
  • varlociraptor-delly/COLO_829-TGen.adhoc.0.98.bcf
  • varlociraptor-delly/COLO_829-EBI.adhoc.0.98.bcf
  • varlociraptor-lancet/COLO_829-GSC.adhoc.0.98.bcf
  • varlociraptor-lancet/COLO_829-Ill.adhoc.0.98.bcf
  • varlociraptor-lancet/COLO_829-TGen.adhoc.0.98.bcf
  • varlociraptor-lancet/COLO_829-EBI.adhoc.0.98.bcf
  • varlociraptor-manta/COLO_829-GSC.adhoc.0.98.bcf
  • varlociraptor-manta/COLO_829-Ill.adhoc.0.98.bcf
  • varlociraptor-manta/COLO_829-TGen.adhoc.0.98.bcf
  • varlociraptor-manta/COLO_829-EBI.adhoc.0.98.bcf
  • varlociraptor-strelka/COLO_829-GSC.adhoc.0.98.bcf
  • varlociraptor-strelka/COLO_829-Ill.adhoc.0.98.bcf
  • varlociraptor-strelka/COLO_829-TGen.adhoc.0.98.bcf
  • varlociraptor-strelka/COLO_829-EBI.adhoc.0.98.bcf
  • varlociraptor-bpi/COLO_829-GSC.adhoc.0.98.bcf
  • varlociraptor-bpi/COLO_829-Ill.adhoc.0.98.bcf
  • varlociraptor-bpi/COLO_829-TGen.adhoc.0.98.bcf
  • varlociraptor-bpi/COLO_829-EBI.adhoc.0.98.bcf
  • bcftools ==1.5
 1
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
varlociraptor_call 600
  • varlociraptor-delly/COLO_829-GSC.1.bcf
  • varlociraptor-delly/COLO_829-GSC.2.bcf
  • varlociraptor-delly/COLO_829-GSC.3.bcf
  • varlociraptor-delly/COLO_829-GSC.4.bcf
  • varlociraptor-delly/COLO_829-GSC.5.bcf
  • varlociraptor-delly/COLO_829-GSC.6.bcf
  • varlociraptor-delly/COLO_829-GSC.7.bcf
  • varlociraptor-delly/COLO_829-GSC.8.bcf
  • varlociraptor-delly/COLO_829-GSC.9.bcf
  • varlociraptor-delly/COLO_829-GSC.10.bcf
  • varlociraptor-delly/COLO_829-GSC.11.bcf
  • varlociraptor-delly/COLO_829-GSC.12.bcf
  • varlociraptor-delly/COLO_829-GSC.13.bcf
  • varlociraptor-delly/COLO_829-GSC.14.bcf
  • varlociraptor-delly/COLO_829-GSC.15.bcf
  • varlociraptor-delly/COLO_829-GSC.16.bcf
  • varlociraptor-delly/COLO_829-GSC.17.bcf
  • varlociraptor-delly/COLO_829-GSC.18.bcf
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  • varlociraptor-strelka/COLO_829-Ill.4.bcf
  • varlociraptor-strelka/COLO_829-Ill.5.bcf
  • varlociraptor-strelka/COLO_829-Ill.6.bcf
  • varlociraptor-strelka/COLO_829-Ill.7.bcf
  • varlociraptor-strelka/COLO_829-Ill.8.bcf
  • varlociraptor-strelka/COLO_829-Ill.9.bcf
  • varlociraptor-strelka/COLO_829-Ill.10.bcf
  • varlociraptor-strelka/COLO_829-Ill.11.bcf
  • varlociraptor-strelka/COLO_829-Ill.12.bcf
  • varlociraptor-strelka/COLO_829-Ill.13.bcf
  • varlociraptor-strelka/COLO_829-Ill.14.bcf
  • varlociraptor-strelka/COLO_829-Ill.15.bcf
  • varlociraptor-strelka/COLO_829-Ill.16.bcf
  • varlociraptor-strelka/COLO_829-Ill.17.bcf
  • varlociraptor-strelka/COLO_829-Ill.18.bcf
  • varlociraptor-strelka/COLO_829-Ill.19.bcf
  • varlociraptor-strelka/COLO_829-Ill.20.bcf
  • varlociraptor-strelka/COLO_829-Ill.21.bcf
  • varlociraptor-strelka/COLO_829-Ill.22.bcf
  • varlociraptor-strelka/COLO_829-Ill.M.bcf
  • varlociraptor-strelka/COLO_829-Ill.X.bcf
  • varlociraptor-strelka/COLO_829-Ill.Y.bcf
  • varlociraptor-strelka/COLO_829-TGen.1.bcf
  • varlociraptor-strelka/COLO_829-TGen.2.bcf
  • varlociraptor-strelka/COLO_829-TGen.3.bcf
  • varlociraptor-strelka/COLO_829-TGen.4.bcf
  • varlociraptor-strelka/COLO_829-TGen.5.bcf
  • varlociraptor-strelka/COLO_829-TGen.6.bcf
  • varlociraptor-strelka/COLO_829-TGen.7.bcf
  • varlociraptor-strelka/COLO_829-TGen.8.bcf
  • varlociraptor-strelka/COLO_829-TGen.9.bcf
  • varlociraptor-strelka/COLO_829-TGen.10.bcf
  • varlociraptor-strelka/COLO_829-TGen.11.bcf
  • varlociraptor-strelka/COLO_829-TGen.12.bcf
  • varlociraptor-strelka/COLO_829-TGen.13.bcf
  • varlociraptor-strelka/COLO_829-TGen.14.bcf
  • varlociraptor-strelka/COLO_829-TGen.15.bcf
  • varlociraptor-strelka/COLO_829-TGen.16.bcf
  • varlociraptor-strelka/COLO_829-TGen.17.bcf
  • varlociraptor-strelka/COLO_829-TGen.18.bcf
  • varlociraptor-strelka/COLO_829-TGen.19.bcf
  • varlociraptor-strelka/COLO_829-TGen.20.bcf
  • varlociraptor-strelka/COLO_829-TGen.21.bcf
  • varlociraptor-strelka/COLO_829-TGen.22.bcf
  • varlociraptor-strelka/COLO_829-TGen.M.bcf
  • varlociraptor-strelka/COLO_829-TGen.X.bcf
  • varlociraptor-strelka/COLO_829-TGen.Y.bcf
  • varlociraptor-strelka/COLO_829-EBI.1.bcf
  • varlociraptor-strelka/COLO_829-EBI.2.bcf
  • varlociraptor-strelka/COLO_829-EBI.3.bcf
  • varlociraptor-strelka/COLO_829-EBI.4.bcf
  • varlociraptor-strelka/COLO_829-EBI.5.bcf
  • varlociraptor-strelka/COLO_829-EBI.6.bcf
  • varlociraptor-strelka/COLO_829-EBI.7.bcf
  • varlociraptor-strelka/COLO_829-EBI.8.bcf
  • varlociraptor-strelka/COLO_829-EBI.9.bcf
  • varlociraptor-strelka/COLO_829-EBI.10.bcf
  • varlociraptor-strelka/COLO_829-EBI.11.bcf
  • varlociraptor-strelka/COLO_829-EBI.12.bcf
  • varlociraptor-strelka/COLO_829-EBI.13.bcf
  • varlociraptor-strelka/COLO_829-EBI.14.bcf
  • varlociraptor-strelka/COLO_829-EBI.15.bcf
  • varlociraptor-strelka/COLO_829-EBI.16.bcf
  • varlociraptor-strelka/COLO_829-EBI.17.bcf
  • varlociraptor-strelka/COLO_829-EBI.18.bcf
  • varlociraptor-strelka/COLO_829-EBI.19.bcf
  • varlociraptor-strelka/COLO_829-EBI.20.bcf
  • varlociraptor-strelka/COLO_829-EBI.21.bcf
  • varlociraptor-strelka/COLO_829-EBI.22.bcf
  • varlociraptor-strelka/COLO_829-EBI.M.bcf
  • varlociraptor-strelka/COLO_829-EBI.X.bcf
  • varlociraptor-strelka/COLO_829-EBI.Y.bcf
  • varlociraptor-bpi/COLO_829-GSC.1.bcf
  • varlociraptor-bpi/COLO_829-GSC.2.bcf
  • varlociraptor-bpi/COLO_829-GSC.3.bcf
  • varlociraptor-bpi/COLO_829-GSC.4.bcf
  • varlociraptor-bpi/COLO_829-GSC.5.bcf
  • varlociraptor-bpi/COLO_829-GSC.6.bcf
  • varlociraptor-bpi/COLO_829-GSC.7.bcf
  • varlociraptor-bpi/COLO_829-GSC.8.bcf
  • varlociraptor-bpi/COLO_829-GSC.9.bcf
  • varlociraptor-bpi/COLO_829-GSC.10.bcf
  • varlociraptor-bpi/COLO_829-GSC.11.bcf
  • varlociraptor-bpi/COLO_829-GSC.12.bcf
  • varlociraptor-bpi/COLO_829-GSC.13.bcf
  • varlociraptor-bpi/COLO_829-GSC.14.bcf
  • varlociraptor-bpi/COLO_829-GSC.15.bcf
  • varlociraptor-bpi/COLO_829-GSC.16.bcf
  • varlociraptor-bpi/COLO_829-GSC.17.bcf
  • varlociraptor-bpi/COLO_829-GSC.18.bcf
  • varlociraptor-bpi/COLO_829-GSC.19.bcf
  • varlociraptor-bpi/COLO_829-GSC.20.bcf
  • varlociraptor-bpi/COLO_829-GSC.21.bcf
  • varlociraptor-bpi/COLO_829-GSC.22.bcf
  • varlociraptor-bpi/COLO_829-GSC.M.bcf
  • varlociraptor-bpi/COLO_829-GSC.X.bcf
  • varlociraptor-bpi/COLO_829-GSC.Y.bcf
  • varlociraptor-bpi/COLO_829-Ill.1.bcf
  • varlociraptor-bpi/COLO_829-Ill.2.bcf
  • varlociraptor-bpi/COLO_829-Ill.3.bcf
  • varlociraptor-bpi/COLO_829-Ill.4.bcf
  • varlociraptor-bpi/COLO_829-Ill.5.bcf
  • varlociraptor-bpi/COLO_829-Ill.6.bcf
  • varlociraptor-bpi/COLO_829-Ill.7.bcf
  • varlociraptor-bpi/COLO_829-Ill.8.bcf
  • varlociraptor-bpi/COLO_829-Ill.9.bcf
  • varlociraptor-bpi/COLO_829-Ill.10.bcf
  • varlociraptor-bpi/COLO_829-Ill.11.bcf
  • varlociraptor-bpi/COLO_829-Ill.12.bcf
  • varlociraptor-bpi/COLO_829-Ill.13.bcf
  • varlociraptor-bpi/COLO_829-Ill.14.bcf
  • varlociraptor-bpi/COLO_829-Ill.15.bcf
  • varlociraptor-bpi/COLO_829-Ill.16.bcf
  • varlociraptor-bpi/COLO_829-Ill.17.bcf
  • varlociraptor-bpi/COLO_829-Ill.18.bcf
  • varlociraptor-bpi/COLO_829-Ill.19.bcf
  • varlociraptor-bpi/COLO_829-Ill.20.bcf
  • varlociraptor-bpi/COLO_829-Ill.21.bcf
  • varlociraptor-bpi/COLO_829-Ill.22.bcf
  • varlociraptor-bpi/COLO_829-Ill.M.bcf
  • varlociraptor-bpi/COLO_829-Ill.X.bcf
  • varlociraptor-bpi/COLO_829-Ill.Y.bcf
  • varlociraptor-bpi/COLO_829-TGen.1.bcf
  • varlociraptor-bpi/COLO_829-TGen.2.bcf
  • varlociraptor-bpi/COLO_829-TGen.3.bcf
  • varlociraptor-bpi/COLO_829-TGen.4.bcf
  • varlociraptor-bpi/COLO_829-TGen.5.bcf
  • varlociraptor-bpi/COLO_829-TGen.6.bcf
  • varlociraptor-bpi/COLO_829-TGen.7.bcf
  • varlociraptor-bpi/COLO_829-TGen.8.bcf
  • varlociraptor-bpi/COLO_829-TGen.9.bcf
  • varlociraptor-bpi/COLO_829-TGen.10.bcf
  • varlociraptor-bpi/COLO_829-TGen.11.bcf
  • varlociraptor-bpi/COLO_829-TGen.12.bcf
  • varlociraptor-bpi/COLO_829-TGen.13.bcf
  • varlociraptor-bpi/COLO_829-TGen.14.bcf
  • varlociraptor-bpi/COLO_829-TGen.15.bcf
  • varlociraptor-bpi/COLO_829-TGen.16.bcf
  • varlociraptor-bpi/COLO_829-TGen.17.bcf
  • varlociraptor-bpi/COLO_829-TGen.18.bcf
  • varlociraptor-bpi/COLO_829-TGen.19.bcf
  • varlociraptor-bpi/COLO_829-TGen.20.bcf
  • varlociraptor-bpi/COLO_829-TGen.21.bcf
  • varlociraptor-bpi/COLO_829-TGen.22.bcf
  • varlociraptor-bpi/COLO_829-TGen.M.bcf
  • varlociraptor-bpi/COLO_829-TGen.X.bcf
  • varlociraptor-bpi/COLO_829-TGen.Y.bcf
  • varlociraptor-bpi/COLO_829-EBI.1.bcf
  • varlociraptor-bpi/COLO_829-EBI.2.bcf
  • varlociraptor-bpi/COLO_829-EBI.3.bcf
  • varlociraptor-bpi/COLO_829-EBI.4.bcf
  • varlociraptor-bpi/COLO_829-EBI.5.bcf
  • varlociraptor-bpi/COLO_829-EBI.6.bcf
  • varlociraptor-bpi/COLO_829-EBI.7.bcf
  • varlociraptor-bpi/COLO_829-EBI.8.bcf
  • varlociraptor-bpi/COLO_829-EBI.9.bcf
  • varlociraptor-bpi/COLO_829-EBI.10.bcf
  • varlociraptor-bpi/COLO_829-EBI.11.bcf
  • varlociraptor-bpi/COLO_829-EBI.12.bcf
  • varlociraptor-bpi/COLO_829-EBI.13.bcf
  • varlociraptor-bpi/COLO_829-EBI.14.bcf
  • varlociraptor-bpi/COLO_829-EBI.15.bcf
  • varlociraptor-bpi/COLO_829-EBI.16.bcf
  • varlociraptor-bpi/COLO_829-EBI.17.bcf
  • varlociraptor-bpi/COLO_829-EBI.18.bcf
  • varlociraptor-bpi/COLO_829-EBI.19.bcf
  • varlociraptor-bpi/COLO_829-EBI.20.bcf
  • varlociraptor-bpi/COLO_829-EBI.21.bcf
  • varlociraptor-bpi/COLO_829-EBI.22.bcf
  • varlociraptor-bpi/COLO_829-EBI.M.bcf
  • varlociraptor-bpi/COLO_829-EBI.X.bcf
  • varlociraptor-bpi/COLO_829-EBI.Y.bcf
  • varlociraptor-delly/simulated-bwa.1.bcf
  • varlociraptor-delly/simulated-bwa.2.bcf
  • varlociraptor-delly/simulated-bwa.3.bcf
  • varlociraptor-delly/simulated-bwa.4.bcf
  • varlociraptor-delly/simulated-bwa.5.bcf
  • varlociraptor-delly/simulated-bwa.6.bcf
  • varlociraptor-delly/simulated-bwa.7.bcf
  • varlociraptor-delly/simulated-bwa.8.bcf
  • varlociraptor-delly/simulated-bwa.9.bcf
  • varlociraptor-delly/simulated-bwa.10.bcf
  • varlociraptor-delly/simulated-bwa.11.bcf
  • varlociraptor-delly/simulated-bwa.12.bcf
  • varlociraptor-delly/simulated-bwa.13.bcf
  • varlociraptor-delly/simulated-bwa.14.bcf
  • varlociraptor-delly/simulated-bwa.15.bcf
  • varlociraptor-delly/simulated-bwa.16.bcf
  • varlociraptor-delly/simulated-bwa.17.bcf
  • varlociraptor-delly/simulated-bwa.18.bcf
  • varlociraptor-delly/simulated-bwa.19.bcf
  • varlociraptor-delly/simulated-bwa.20.bcf
  • varlociraptor-delly/simulated-bwa.21.bcf
  • varlociraptor-delly/simulated-bwa.22.bcf
  • varlociraptor-delly/simulated-bwa.M.bcf
  • varlociraptor-delly/simulated-bwa.X.bcf
  • varlociraptor-delly/simulated-bwa.Y.bcf
  • varlociraptor-lancet/simulated-bwa.1.bcf
  • varlociraptor-lancet/simulated-bwa.2.bcf
  • varlociraptor-lancet/simulated-bwa.3.bcf
  • varlociraptor-lancet/simulated-bwa.4.bcf
  • varlociraptor-lancet/simulated-bwa.5.bcf
  • varlociraptor-lancet/simulated-bwa.6.bcf
  • varlociraptor-lancet/simulated-bwa.7.bcf
  • varlociraptor-lancet/simulated-bwa.8.bcf
  • varlociraptor-lancet/simulated-bwa.9.bcf
  • varlociraptor-lancet/simulated-bwa.10.bcf
  • varlociraptor-lancet/simulated-bwa.11.bcf
  • varlociraptor-lancet/simulated-bwa.12.bcf
  • varlociraptor-lancet/simulated-bwa.13.bcf
  • varlociraptor-lancet/simulated-bwa.14.bcf
  • varlociraptor-lancet/simulated-bwa.15.bcf
  • varlociraptor-lancet/simulated-bwa.16.bcf
  • varlociraptor-lancet/simulated-bwa.17.bcf
  • varlociraptor-lancet/simulated-bwa.18.bcf
  • varlociraptor-lancet/simulated-bwa.19.bcf
  • varlociraptor-lancet/simulated-bwa.20.bcf
  • varlociraptor-lancet/simulated-bwa.21.bcf
  • varlociraptor-lancet/simulated-bwa.22.bcf
  • varlociraptor-lancet/simulated-bwa.M.bcf
  • varlociraptor-lancet/simulated-bwa.X.bcf
  • varlociraptor-lancet/simulated-bwa.Y.bcf
  • varlociraptor-manta/simulated-bwa.1.bcf
  • varlociraptor-manta/simulated-bwa.2.bcf
  • varlociraptor-manta/simulated-bwa.3.bcf
  • varlociraptor-manta/simulated-bwa.4.bcf
  • varlociraptor-manta/simulated-bwa.5.bcf
  • varlociraptor-manta/simulated-bwa.6.bcf
  • varlociraptor-manta/simulated-bwa.7.bcf
  • varlociraptor-manta/simulated-bwa.8.bcf
  • varlociraptor-manta/simulated-bwa.9.bcf
  • varlociraptor-manta/simulated-bwa.10.bcf
  • varlociraptor-manta/simulated-bwa.11.bcf
  • varlociraptor-manta/simulated-bwa.12.bcf
  • varlociraptor-manta/simulated-bwa.13.bcf
  • varlociraptor-manta/simulated-bwa.14.bcf
  • varlociraptor-manta/simulated-bwa.15.bcf
  • varlociraptor-manta/simulated-bwa.16.bcf
  • varlociraptor-manta/simulated-bwa.17.bcf
  • varlociraptor-manta/simulated-bwa.18.bcf
  • varlociraptor-manta/simulated-bwa.19.bcf
  • varlociraptor-manta/simulated-bwa.20.bcf
  • varlociraptor-manta/simulated-bwa.21.bcf
  • varlociraptor-manta/simulated-bwa.22.bcf
  • varlociraptor-manta/simulated-bwa.M.bcf
  • varlociraptor-manta/simulated-bwa.X.bcf
  • varlociraptor-manta/simulated-bwa.Y.bcf
  • varlociraptor-strelka/simulated-bwa.1.bcf
  • varlociraptor-strelka/simulated-bwa.2.bcf
  • varlociraptor-strelka/simulated-bwa.3.bcf
  • varlociraptor-strelka/simulated-bwa.4.bcf
  • varlociraptor-strelka/simulated-bwa.5.bcf
  • varlociraptor-strelka/simulated-bwa.6.bcf
  • varlociraptor-strelka/simulated-bwa.7.bcf
  • varlociraptor-strelka/simulated-bwa.8.bcf
  • varlociraptor-strelka/simulated-bwa.9.bcf
  • varlociraptor-strelka/simulated-bwa.10.bcf
  • varlociraptor-strelka/simulated-bwa.11.bcf
  • varlociraptor-strelka/simulated-bwa.12.bcf
  • varlociraptor-strelka/simulated-bwa.13.bcf
  • varlociraptor-strelka/simulated-bwa.14.bcf
  • varlociraptor-strelka/simulated-bwa.15.bcf
  • varlociraptor-strelka/simulated-bwa.16.bcf
  • varlociraptor-strelka/simulated-bwa.17.bcf
  • varlociraptor-strelka/simulated-bwa.18.bcf
  • varlociraptor-strelka/simulated-bwa.19.bcf
  • varlociraptor-strelka/simulated-bwa.20.bcf
  • varlociraptor-strelka/simulated-bwa.21.bcf
  • varlociraptor-strelka/simulated-bwa.22.bcf
  • varlociraptor-strelka/simulated-bwa.M.bcf
  • varlociraptor-strelka/simulated-bwa.X.bcf
  • varlociraptor-strelka/simulated-bwa.Y.bcf
1
bcftools view -Ou {input.calls} {params.chrom_prefix} | varlociraptor call variants {input.ref} {config[caller][varlociraptor][params]} {params.caller} tumor-normal {input.bams} --purity {params.purity} > {output} 2> {log}
delly_adhoc 4
  • adhoc-delly/COLO_829-GSC.all.bcf
  • adhoc-delly/COLO_829-Ill.all.bcf
  • adhoc-delly/COLO_829-TGen.all.bcf
  • adhoc-delly/COLO_829-EBI.all.bcf
  • delly =0.7.7
  • bcftools =1.6
1
delly filter -m 0 -r 1.0 --samples {input.samples} -o {params.tmp} {input.bcf}; bcftools view -i INFO/SOMATIC -f PASS -Ob {params.tmp} > {output}
lancet_adhoc 4
  • adhoc-lancet/COLO_829-GSC.all.bcf
  • adhoc-lancet/COLO_829-Ill.all.bcf
  • adhoc-lancet/COLO_829-TGen.all.bcf
  • adhoc-lancet/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
manta_adhoc 4
  • adhoc-manta/COLO_829-GSC.all.bcf
  • adhoc-manta/COLO_829-Ill.all.bcf
  • adhoc-manta/COLO_829-TGen.all.bcf
  • adhoc-manta/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
strelka_adhoc 4
  • adhoc-strelka/COLO_829-GSC.all.bcf
  • adhoc-strelka/COLO_829-Ill.all.bcf
  • adhoc-strelka/COLO_829-TGen.all.bcf
  • adhoc-strelka/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
bpi_adhoc 4
  • adhoc-bpi/COLO_829-GSC.all.bcf
  • adhoc-bpi/COLO_829-Ill.all.bcf
  • adhoc-bpi/COLO_829-TGen.all.bcf
  • adhoc-bpi/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
delly_concat 4
  • delly/COLO_829-GSC.all.bcf
  • delly/COLO_829-Ill.all.bcf
  • delly/COLO_829-TGen.all.bcf
  • delly/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools concat {snakemake.params} -o {snakemake.output[0]} "
    "{snakemake.input}")
index_bcf 20
  • delly/COLO_829-GSC.all.bcf.csi
  • delly/COLO_829-Ill.all.bcf.csi
  • delly/COLO_829-TGen.all.bcf.csi
  • delly/COLO_829-EBI.all.bcf.csi
  • default-lancet/COLO_829-GSC.all.bcf.csi
  • default-lancet/COLO_829-Ill.all.bcf.csi
  • default-lancet/COLO_829-TGen.all.bcf.csi
  • default-lancet/COLO_829-EBI.all.bcf.csi
  • manta/COLO_829-GSC.all.bcf.csi
  • manta/COLO_829-Ill.all.bcf.csi
  • manta/COLO_829-TGen.all.bcf.csi
  • manta/COLO_829-EBI.all.bcf.csi
  • default-strelka/COLO_829-GSC.all.bcf.csi
  • default-strelka/COLO_829-Ill.all.bcf.csi
  • default-strelka/COLO_829-TGen.all.bcf.csi
  • default-strelka/COLO_829-EBI.all.bcf.csi
  • bpi/COLO_829-GSC.all.bcf.csi
  • bpi/COLO_829-Ill.all.bcf.csi
  • bpi/COLO_829-TGen.all.bcf.csi
  • bpi/COLO_829-EBI.all.bcf.csi
  • bcftools =1.6
  • samtools =1.6
1
bcftools index {input}
mark_duplicates 8
  • mapped-bwa/COLO_829-GSC.tumor.hg38.sorted.bam
  • mapped-bwa/COLO_829-GSC.tumor.hg38.markdup.metrics.txt
  • mapped-bwa/COLO_829-GSC.normal.hg38.sorted.bam
  • mapped-bwa/COLO_829-GSC.normal.hg38.markdup.metrics.txt
  • mapped-bwa/COLO_829-Ill.tumor.hg38.sorted.bam
  • mapped-bwa/COLO_829-Ill.tumor.hg38.markdup.metrics.txt
  • mapped-bwa/COLO_829-Ill.normal.hg38.sorted.bam
  • mapped-bwa/COLO_829-Ill.normal.hg38.markdup.metrics.txt
  • mapped-bwa/COLO_829-TGen.tumor.hg38.sorted.bam
  • mapped-bwa/COLO_829-TGen.tumor.hg38.markdup.metrics.txt
  • mapped-bwa/COLO_829-TGen.normal.hg38.sorted.bam
  • mapped-bwa/COLO_829-TGen.normal.hg38.markdup.metrics.txt
  • mapped-bwa/COLO_829-EBI.tumor.hg38.sorted.bam
  • mapped-bwa/COLO_829-EBI.tumor.hg38.markdup.metrics.txt
  • mapped-bwa/COLO_829-EBI.normal.hg38.sorted.bam
  • mapped-bwa/COLO_829-EBI.normal.hg38.markdup.metrics.txt
  • picard ==2.9.2
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell("picard MarkDuplicates {snakemake.params} INPUT={snakemake.input} "
      "OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
      "&> {snakemake.log}")
samtools_index 8
  • mapped-bwa/COLO_829-GSC.tumor.hg38.sorted.bam.bai
  • mapped-bwa/COLO_829-GSC.normal.hg38.sorted.bam.bai
  • mapped-bwa/COLO_829-Ill.tumor.hg38.sorted.bam.bai
  • mapped-bwa/COLO_829-Ill.normal.hg38.sorted.bam.bai
  • mapped-bwa/COLO_829-TGen.tumor.hg38.sorted.bam.bai
  • mapped-bwa/COLO_829-TGen.normal.hg38.sorted.bam.bai
  • mapped-bwa/COLO_829-EBI.tumor.hg38.sorted.bam.bai
  • mapped-bwa/COLO_829-EBI.normal.hg38.sorted.bam.bai
  • samtools ==1.6
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell("samtools index {snakemake.params} {snakemake.input[0]} {snakemake.output[0]}")
merge_lancet 4
  • default-lancet/COLO_829-GSC.all.bcf
  • default-lancet/COLO_829-Ill.all.bcf
  • default-lancet/COLO_829-TGen.all.bcf
  • default-lancet/COLO_829-EBI.all.bcf
  • bcftools =1.6
  • samtools =1.6
1
bcftools concat -Ob {input} > {output}
manta_raw 4
  • manta/COLO_829-GSC.all.bcf
  • manta/COLO_829-Ill.all.bcf
  • manta/COLO_829-TGen.all.bcf
  • manta/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
strelka_default 4
  • default-strelka/COLO_829-GSC.all.bcf
  • default-strelka/COLO_829-Ill.all.bcf
  • default-strelka/COLO_829-TGen.all.bcf
  • default-strelka/COLO_829-EBI.all.bcf
  • bcftools ==1.6
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools concat {snakemake.params} -o {snakemake.output[0]} "
    "{snakemake.input.calls}")
bpi_convert 4
  • bpi/COLO_829-GSC.all.bcf
  • bpi/COLO_829-Ill.all.bcf
  • bpi/COLO_829-TGen.all.bcf
  • bpi/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
manta_default 4
  • default-manta/COLO_829-GSC.all.bcf
  • default-manta/COLO_829-Ill.all.bcf
  • default-manta/COLO_829-TGen.all.bcf
  • default-manta/COLO_829-EBI.all.bcf
  • bcftools ==1.5
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell(
    "bcftools view {snakemake.params} {snakemake.input[0]} "
    "-o {snakemake.output[0]}")
delly 8
  • delly/COLO_829-GSC.DEL.bcf
  • delly/COLO_829-GSC.INS.bcf
  • delly/COLO_829-Ill.DEL.bcf
  • delly/COLO_829-Ill.INS.bcf
  • delly/COLO_829-TGen.DEL.bcf
  • delly/COLO_829-TGen.INS.bcf
  • delly/COLO_829-EBI.DEL.bcf
  • delly/COLO_829-EBI.INS.bcf
  • delly ==0.7.7
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


try:
    exclude = "-x " + snakemake.input.exclude
except AttributeError:
    exclude = ""


extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "OMP_NUM_THREADS={snakemake.threads} delly call {extra} "
    "{exclude} -t {snakemake.params.vartype} -g {snakemake.input.ref} "
    "-o {snakemake.output[0]} {snakemake.input.samples} {log}")
samtools_sort 8
  • mapped-bwa/COLO_829-GSC.tumor.hg38.sorted.pre.bam
  • mapped-bwa/COLO_829-GSC.normal.hg38.sorted.pre.bam
  • mapped-bwa/COLO_829-Ill.tumor.hg38.sorted.pre.bam
  • mapped-bwa/COLO_829-Ill.normal.hg38.sorted.pre.bam
  • mapped-bwa/COLO_829-TGen.tumor.hg38.sorted.pre.bam
  • mapped-bwa/COLO_829-TGen.normal.hg38.sorted.pre.bam
  • mapped-bwa/COLO_829-EBI.tumor.hg38.sorted.pre.bam
  • mapped-bwa/COLO_829-EBI.normal.hg38.sorted.pre.bam
  • samtools ==1.6
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


import os
from snakemake.shell import shell


prefix = os.path.splitext(snakemake.output[0])[0]

shell(
    "samtools sort {snakemake.params} -@ {snakemake.threads} -o {snakemake.output[0]} "
    "-T {prefix} {snakemake.input[0]}")
fix_lancet 100
  • lancet/COLO_829-GSC/chr1.fixed.vcf
  • lancet/COLO_829-GSC/chr2.fixed.vcf
  • lancet/COLO_829-GSC/chr3.fixed.vcf
  • lancet/COLO_829-GSC/chr4.fixed.vcf
  • lancet/COLO_829-GSC/chr5.fixed.vcf
  • lancet/COLO_829-GSC/chr6.fixed.vcf
  • lancet/COLO_829-GSC/chr7.fixed.vcf
  • lancet/COLO_829-GSC/chr8.fixed.vcf
  • lancet/COLO_829-GSC/chr9.fixed.vcf
  • lancet/COLO_829-GSC/chr10.fixed.vcf
  • lancet/COLO_829-GSC/chr11.fixed.vcf
  • lancet/COLO_829-GSC/chr12.fixed.vcf
  • lancet/COLO_829-GSC/chr13.fixed.vcf
  • lancet/COLO_829-GSC/chr14.fixed.vcf
  • lancet/COLO_829-GSC/chr15.fixed.vcf
  • lancet/COLO_829-GSC/chr16.fixed.vcf
  • lancet/COLO_829-GSC/chr17.fixed.vcf
  • lancet/COLO_829-GSC/chr18.fixed.vcf
  • lancet/COLO_829-GSC/chr19.fixed.vcf
  • lancet/COLO_829-GSC/chr20.fixed.vcf
  • lancet/COLO_829-GSC/chr21.fixed.vcf
  • lancet/COLO_829-GSC/chr22.fixed.vcf
  • lancet/COLO_829-GSC/chrM.fixed.vcf
  • lancet/COLO_829-GSC/chrX.fixed.vcf
  • lancet/COLO_829-GSC/chrY.fixed.vcf
  • lancet/COLO_829-Ill/chr1.fixed.vcf
  • lancet/COLO_829-Ill/chr2.fixed.vcf
  • lancet/COLO_829-Ill/chr3.fixed.vcf
  • lancet/COLO_829-Ill/chr4.fixed.vcf
  • lancet/COLO_829-Ill/chr5.fixed.vcf
  • lancet/COLO_829-Ill/chr6.fixed.vcf
  • lancet/COLO_829-Ill/chr7.fixed.vcf
  • lancet/COLO_829-Ill/chr8.fixed.vcf
  • lancet/COLO_829-Ill/chr9.fixed.vcf
  • lancet/COLO_829-Ill/chr10.fixed.vcf
  • lancet/COLO_829-Ill/chr11.fixed.vcf
  • lancet/COLO_829-Ill/chr12.fixed.vcf
  • lancet/COLO_829-Ill/chr13.fixed.vcf
  • lancet/COLO_829-Ill/chr14.fixed.vcf
  • lancet/COLO_829-Ill/chr15.fixed.vcf
  • lancet/COLO_829-Ill/chr16.fixed.vcf
  • lancet/COLO_829-Ill/chr17.fixed.vcf
  • lancet/COLO_829-Ill/chr18.fixed.vcf
  • lancet/COLO_829-Ill/chr19.fixed.vcf
  • lancet/COLO_829-Ill/chr20.fixed.vcf
  • lancet/COLO_829-Ill/chr21.fixed.vcf
  • lancet/COLO_829-Ill/chr22.fixed.vcf
  • lancet/COLO_829-Ill/chrM.fixed.vcf
  • lancet/COLO_829-Ill/chrX.fixed.vcf
  • lancet/COLO_829-Ill/chrY.fixed.vcf
  • lancet/COLO_829-TGen/chr1.fixed.vcf
  • lancet/COLO_829-TGen/chr2.fixed.vcf
  • lancet/COLO_829-TGen/chr3.fixed.vcf
  • lancet/COLO_829-TGen/chr4.fixed.vcf
  • lancet/COLO_829-TGen/chr5.fixed.vcf
  • lancet/COLO_829-TGen/chr6.fixed.vcf
  • lancet/COLO_829-TGen/chr7.fixed.vcf
  • lancet/COLO_829-TGen/chr8.fixed.vcf
  • lancet/COLO_829-TGen/chr9.fixed.vcf
  • lancet/COLO_829-TGen/chr10.fixed.vcf
  • lancet/COLO_829-TGen/chr11.fixed.vcf
  • lancet/COLO_829-TGen/chr12.fixed.vcf
  • lancet/COLO_829-TGen/chr13.fixed.vcf
  • lancet/COLO_829-TGen/chr14.fixed.vcf
  • lancet/COLO_829-TGen/chr15.fixed.vcf
  • lancet/COLO_829-TGen/chr16.fixed.vcf
  • lancet/COLO_829-TGen/chr17.fixed.vcf
  • lancet/COLO_829-TGen/chr18.fixed.vcf
  • lancet/COLO_829-TGen/chr19.fixed.vcf
  • lancet/COLO_829-TGen/chr20.fixed.vcf
  • lancet/COLO_829-TGen/chr21.fixed.vcf
  • lancet/COLO_829-TGen/chr22.fixed.vcf
  • lancet/COLO_829-TGen/chrM.fixed.vcf
  • lancet/COLO_829-TGen/chrX.fixed.vcf
  • lancet/COLO_829-TGen/chrY.fixed.vcf
  • lancet/COLO_829-EBI/chr1.fixed.vcf
  • lancet/COLO_829-EBI/chr2.fixed.vcf
  • lancet/COLO_829-EBI/chr3.fixed.vcf
  • lancet/COLO_829-EBI/chr4.fixed.vcf
  • lancet/COLO_829-EBI/chr5.fixed.vcf
  • lancet/COLO_829-EBI/chr6.fixed.vcf
  • lancet/COLO_829-EBI/chr7.fixed.vcf
  • lancet/COLO_829-EBI/chr8.fixed.vcf
  • lancet/COLO_829-EBI/chr9.fixed.vcf
  • lancet/COLO_829-EBI/chr10.fixed.vcf
  • lancet/COLO_829-EBI/chr11.fixed.vcf
  • lancet/COLO_829-EBI/chr12.fixed.vcf
  • lancet/COLO_829-EBI/chr13.fixed.vcf
  • lancet/COLO_829-EBI/chr14.fixed.vcf
  • lancet/COLO_829-EBI/chr15.fixed.vcf
  • lancet/COLO_829-EBI/chr16.fixed.vcf
  • lancet/COLO_829-EBI/chr17.fixed.vcf
  • lancet/COLO_829-EBI/chr18.fixed.vcf
  • lancet/COLO_829-EBI/chr19.fixed.vcf
  • lancet/COLO_829-EBI/chr20.fixed.vcf
  • lancet/COLO_829-EBI/chr21.fixed.vcf
  • lancet/COLO_829-EBI/chr22.fixed.vcf
  • lancet/COLO_829-EBI/chrM.fixed.vcf
  • lancet/COLO_829-EBI/chrX.fixed.vcf
  • lancet/COLO_829-EBI/chrY.fixed.vcf
  • bcftools =1.6
  • samtools =1.6
1
sed -r 's/MS\=[0-9]+[ACGT]+/MS/g' {input.vcf} | bcftools annotate -o {output} -h {input.header} -
manta 4
  • manta/COLO_829-GSC/results/variants/candidateSV.vcf.gz
  • manta/COLO_829-GSC/results/variants/somaticSV.vcf.gz
  • manta/COLO_829-GSC/results/variants/candidateSmallIndels.vcf.gz
  • manta/COLO_829-Ill/results/variants/candidateSV.vcf.gz
  • manta/COLO_829-Ill/results/variants/somaticSV.vcf.gz
  • manta/COLO_829-Ill/results/variants/candidateSmallIndels.vcf.gz
  • manta/COLO_829-TGen/results/variants/candidateSV.vcf.gz
  • manta/COLO_829-TGen/results/variants/somaticSV.vcf.gz
  • manta/COLO_829-TGen/results/variants/candidateSmallIndels.vcf.gz
  • manta/COLO_829-EBI/results/variants/candidateSV.vcf.gz
  • manta/COLO_829-EBI/results/variants/somaticSV.vcf.gz
  • manta/COLO_829-EBI/results/variants/candidateSmallIndels.vcf.gz
  • manta =1.3.0
1
rm -rf {params.dir}; (configManta.py {params.extra} --tumorBam {input.samples[0]} --normalBam {input.samples[1]} --referenceFasta {input.ref} --runDir {params.dir}; {params.dir}/runWorkflow.py -m local -j {threads}) > {log} 2>&1
strelka 4
  • strelka/COLO_829-GSC/results/variants/somatic.snvs.vcf.gz
  • strelka/COLO_829-GSC/results/variants/somatic.indels.vcf.gz
  • strelka/COLO_829-Ill/results/variants/somatic.snvs.vcf.gz
  • strelka/COLO_829-Ill/results/variants/somatic.indels.vcf.gz
  • strelka/COLO_829-TGen/results/variants/somatic.snvs.vcf.gz
  • strelka/COLO_829-TGen/results/variants/somatic.indels.vcf.gz
  • strelka/COLO_829-EBI/results/variants/somatic.snvs.vcf.gz
  • strelka/COLO_829-EBI/results/variants/somatic.indels.vcf.gz
  • strelka =2.8.4
1
rm -rf {params.dir}; (configureStrelkaSomaticWorkflow.py {params.extra} --tumorBam {input.samples[0]} --normalBam {input.samples[1]} --referenceFasta {input.ref} --runDir {params.dir} --indelCandidates {input.manta}; {params.dir}/runWorkflow.py -m local -j {threads}) > {log} 2>&1
bpi 4
  • bpi/COLO_829-GSC.all.vcf
  • bpi/COLO_829-Ill.all.vcf
  • bpi/COLO_829-TGen.all.vcf
  • bpi/COLO_829-EBI.all.vcf
  • break-point-inspector =1.5
1
(break-point-inspector -vcf {input.manta} -ref {input.samples[1]} -tumor {input.samples[0]} -output_vcf {output}) > {log} 2>&1
bwa 8
  • mapped-bwa/COLO_829-GSC.tumor.hg38.bam
  • mapped-bwa/COLO_829-GSC.normal.hg38.bam
  • mapped-bwa/COLO_829-Ill.tumor.hg38.bam
  • mapped-bwa/COLO_829-Ill.normal.hg38.bam
  • mapped-bwa/COLO_829-TGen.tumor.hg38.bam
  • mapped-bwa/COLO_829-TGen.normal.hg38.bam
  • mapped-bwa/COLO_829-EBI.tumor.hg38.bam
  • mapped-bwa/COLO_829-EBI.normal.hg38.bam
  • python
  • samtools =1.6
  • numpy
  • scikit-learn
  • pandas
  • setuptools
1
(resources/bwa mem -t {threads} {params.extra} {params.index} {input.sample} | samtools view -Sb - > {output}) 2> {log}
lancet 75
  • lancet/COLO_829-GSC/chr1.vcf
  • lancet/COLO_829-GSC/chr2.vcf
  • lancet/COLO_829-GSC/chr3.vcf
  • lancet/COLO_829-GSC/chr4.vcf
  • lancet/COLO_829-GSC/chr5.vcf
  • lancet/COLO_829-GSC/chr6.vcf
  • lancet/COLO_829-GSC/chr7.vcf
  • lancet/COLO_829-GSC/chr8.vcf
  • lancet/COLO_829-GSC/chr9.vcf
  • lancet/COLO_829-GSC/chr10.vcf
  • lancet/COLO_829-GSC/chr11.vcf
  • lancet/COLO_829-GSC/chr12.vcf
  • lancet/COLO_829-GSC/chr13.vcf
  • lancet/COLO_829-GSC/chr14.vcf
  • lancet/COLO_829-GSC/chr15.vcf
  • lancet/COLO_829-GSC/chr16.vcf
  • lancet/COLO_829-GSC/chr17.vcf
  • lancet/COLO_829-GSC/chr18.vcf
  • lancet/COLO_829-GSC/chr19.vcf
  • lancet/COLO_829-GSC/chr20.vcf
  • lancet/COLO_829-GSC/chr21.vcf
  • lancet/COLO_829-GSC/chr22.vcf
  • lancet/COLO_829-GSC/chrM.vcf
  • lancet/COLO_829-GSC/chrX.vcf
  • lancet/COLO_829-GSC/chrY.vcf
  • lancet/COLO_829-Ill/chr1.vcf
  • lancet/COLO_829-Ill/chr2.vcf
  • lancet/COLO_829-Ill/chr3.vcf
  • lancet/COLO_829-Ill/chr4.vcf
  • lancet/COLO_829-Ill/chr5.vcf
  • lancet/COLO_829-Ill/chr6.vcf
  • lancet/COLO_829-Ill/chr7.vcf
  • lancet/COLO_829-Ill/chr8.vcf
  • lancet/COLO_829-Ill/chr9.vcf
  • lancet/COLO_829-Ill/chr10.vcf
  • lancet/COLO_829-Ill/chr11.vcf
  • lancet/COLO_829-Ill/chr12.vcf
  • lancet/COLO_829-Ill/chr13.vcf
  • lancet/COLO_829-Ill/chr14.vcf
  • lancet/COLO_829-Ill/chr15.vcf
  • lancet/COLO_829-Ill/chr16.vcf
  • lancet/COLO_829-Ill/chr17.vcf
  • lancet/COLO_829-Ill/chr18.vcf
  • lancet/COLO_829-Ill/chr19.vcf
  • lancet/COLO_829-Ill/chr20.vcf
  • lancet/COLO_829-Ill/chr21.vcf
  • lancet/COLO_829-Ill/chr22.vcf
  • lancet/COLO_829-Ill/chrM.vcf
  • lancet/COLO_829-Ill/chrX.vcf
  • lancet/COLO_829-Ill/chrY.vcf
  • lancet/COLO_829-TGen/chr1.vcf
  • lancet/COLO_829-TGen/chr2.vcf
  • lancet/COLO_829-TGen/chr3.vcf
  • lancet/COLO_829-TGen/chr4.vcf
  • lancet/COLO_829-TGen/chr5.vcf
  • lancet/COLO_829-TGen/chr6.vcf
  • lancet/COLO_829-TGen/chr7.vcf
  • lancet/COLO_829-TGen/chr8.vcf
  • lancet/COLO_829-TGen/chr9.vcf
  • lancet/COLO_829-TGen/chr10.vcf
  • lancet/COLO_829-TGen/chr11.vcf
  • lancet/COLO_829-TGen/chr12.vcf
  • lancet/COLO_829-TGen/chr13.vcf
  • lancet/COLO_829-TGen/chr14.vcf
  • lancet/COLO_829-TGen/chr15.vcf
  • lancet/COLO_829-TGen/chr16.vcf
  • lancet/COLO_829-TGen/chr17.vcf
  • lancet/COLO_829-TGen/chr18.vcf
  • lancet/COLO_829-TGen/chr19.vcf
  • lancet/COLO_829-TGen/chr20.vcf
  • lancet/COLO_829-TGen/chr21.vcf
  • lancet/COLO_829-TGen/chr22.vcf
  • lancet/COLO_829-TGen/chrM.vcf
  • lancet/COLO_829-TGen/chrX.vcf
  • lancet/COLO_829-TGen/chrY.vcf
  • bamtools =2.3.0
1
LD_LIBRARY_PATH=$CONDA_PREFIX/lib resources/lancet --tumor {input.bams[0]} --normal {input.bams[1]} --ref {input.ref} --reg {params.region} --num-threads {threads} {params.extra} > {output} 2> {log}
lancet 25
  • lancet/COLO_829-EBI/chr1.vcf
  • lancet/COLO_829-EBI/chr2.vcf
  • lancet/COLO_829-EBI/chr3.vcf
  • lancet/COLO_829-EBI/chr4.vcf
  • lancet/COLO_829-EBI/chr5.vcf
  • lancet/COLO_829-EBI/chr6.vcf
  • lancet/COLO_829-EBI/chr7.vcf
  • lancet/COLO_829-EBI/chr8.vcf
  • lancet/COLO_829-EBI/chr9.vcf
  • lancet/COLO_829-EBI/chr10.vcf
  • lancet/COLO_829-EBI/chr11.vcf
  • lancet/COLO_829-EBI/chr12.vcf
  • lancet/COLO_829-EBI/chr13.vcf
  • lancet/COLO_829-EBI/chr14.vcf
  • lancet/COLO_829-EBI/chr15.vcf
  • lancet/COLO_829-EBI/chr16.vcf
  • lancet/COLO_829-EBI/chr17.vcf
  • lancet/COLO_829-EBI/chr18.vcf
  • lancet/COLO_829-EBI/chr19.vcf
  • lancet/COLO_829-EBI/chr20.vcf
  • lancet/COLO_829-EBI/chr21.vcf
  • lancet/COLO_829-EBI/chr22.vcf
  • lancet/COLO_829-EBI/chrM.vcf
  • lancet/COLO_829-EBI/chrX.vcf
  • lancet/COLO_829-EBI/chrY.vcf
1
LD_LIBRARY_PATH=$CONDA_PREFIX/lib resources/lancet --tumor {input.bams[0]} --normal {input.bams[1]} --ref {input.ref} --reg {params.region} --num-threads {threads} {params.extra} > {output} 2> {log}
bam2fq 4
  • reads/COLO_829-Ill.tumor.1.fastq.gz
  • reads/COLO_829-Ill.tumor.2.fastq.gz
  • reads/COLO_829-Ill.tumor.fastq.gz
  • reads/COLO_829-Ill.normal.1.fastq.gz
  • reads/COLO_829-Ill.normal.2.fastq.gz
  • reads/COLO_829-Ill.normal.fastq.gz
  • reads/COLO_829-TGen.tumor.1.fastq.gz
  • reads/COLO_829-TGen.tumor.2.fastq.gz
  • reads/COLO_829-TGen.tumor.fastq.gz
  • reads/COLO_829-TGen.normal.1.fastq.gz
  • reads/COLO_829-TGen.normal.2.fastq.gz
  • reads/COLO_829-TGen.normal.fastq.gz
  • bcftools =1.6
  • samtools =1.6
1
samtools bam2fq {input} -1 {output.m1} -2 {output.m2} -0 {output.mixed}
prepare_bam 8
  • reads/COLO_829-GSC.tumor.namesorted.bam
  • reads/COLO_829-GSC.normal.namesorted.bam
  • reads/COLO_829-Ill.tumor.namesorted.bam
  • reads/COLO_829-Ill.normal.namesorted.bam
  • reads/COLO_829-TGen.tumor.namesorted.bam
  • reads/COLO_829-TGen.normal.namesorted.bam
  • reads/COLO_829-EBI.tumor.namesorted.bam
  • reads/COLO_829-EBI.normal.namesorted.bam
  • samtools ==1.6
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__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


import os
from snakemake.shell import shell


prefix = os.path.splitext(snakemake.output[0])[0]

shell(
    "samtools sort {snakemake.params} -@ {snakemake.threads} -o {snakemake.output[0]} "
    "-T {prefix} {snakemake.input[0]}")