GATK CALCULATECONTAMINATION

Calculate the fraction of reads coming from cross-sample contamination

URL: https://gatk.broadinstitute.org/hc/en-us/articles/360036888972-CalculateContamination

Example

This wrapper can be used in the following way:

rule test_gatk_calculate_contamination:
    input:
        tumor="pileups.table",
        # normal="normal.pileups.table",
    output:
        "contamination.table",
    threads: 1
    resources:
        mem_mb=1024,
    log:
        "logs/gatk/contamination.log",
    params:
        extra="",
    wrapper:
        "v3.9.0/bio/gatk/calculatecontamination"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• gatk4=4.5.0.0

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• tumor: Path to pileup table from GATK GetPileupSummaries

• normal: Optional path to noram pileup table

Output:

• Path to contamination table

Params

• java_opts: param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).

• extra: param allows for additional program arguments.

Authors

• Thibault Dayris

Code

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2023, Thibault Dayris"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"


import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

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

if snakemake.input.get("normal"):
    extra += f" --matched-normal {snakemake.input.normal}"

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' CalculateContamination"
        " --input {snakemake.input.tumor}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output}"
        " {log}"
    )