GATK MUTECT2¶
Call somatic SNVs and indels via local assembly of haplotypes
Software dependencies¶
- gatk4 ==4.1.4.1
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
log:
"logs/mutect_{sample}.log"
wrapper:
"0.65.0/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.
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
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
shell(
"gatk Mutect2 " # Tool and its subprocess
"--input {snakemake.input.map} " # Path to input mapping file
"--output {snakemake.output.vcf} " # Path to output vcf file
"--reference {snakemake.input.fasta} " # Path to reference fasta file
"{extra} " # Extra parameters
"{log}" # Logging behaviour
)