GATK MUTECT2

Call somatic SNVs and indels via local assembly of haplotypes

URL:

Example

This wrapper can be used in the following way:

rule mutect2:
    input:
        fasta = "genome/genome.fasta",
        map = "mapped/{sample}.bam"
    output:
        vcf = "variant/{sample}.vcf"
    message:
        "Testing Mutect2 with {wildcards.sample}"
    threads:
        1
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024
    log:
        "logs/mutect_{sample}.log"
    wrapper:
         "v1.1.0/bio/gatk/mutect"

rule mutect2_bam:
    input:
        fasta = "genome/genome.fasta",
        map = "mapped/{sample}.bam"
    output:
        vcf = "variant_bam/{sample}.vcf",
        bam = "variant_bam/{sample}.bam"
    message:
        "Testing Mutect2 with {wildcards.sample}"
    threads:
        1
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024
    log:
        "logs/mutect_{sample}.log"
    wrapper:
         "v1.1.0/bio/gatk/mutect"

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==4.1.4.1
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• Mapped reads (SAM/BAM/CRAM)
• Reference Fasta file

Output:

• Variant file

Authors

• Thibault Dayris

Code

"""Snakemake wrapper for GATK4 Mutect2"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2019, Dayris Thibault"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake.utils import makedirs
from snakemake_wrapper_utils.java import get_java_opts

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

bam_output = "--bam-output"
if snakemake.output.get("bam", None) is not None:
    bam_output = bam_output + " " + snakemake.output.bam
else:
    bam_output = ""

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

shell(
    "gatk --java-options '{java_opts}' Mutect2 "  # Tool and its subprocess
    "--input {snakemake.input.map} "  # Path to input mapping file
    "{bam_output} "  # Path to output bam file, optional
    "--output {snakemake.output.vcf} "  # Path to output vcf file
    "--reference {snakemake.input.fasta} "  # Path to reference fasta file
    "{extra} "  # Extra parameters
    "{log}"  # Logging behaviour
)