GATK HAPLOTYPECALLER

Run gatk HaplotypeCaller.

Software dependencies

  • gatk4 ==4.0.5.1

Example

This wrapper can be used in the following way:

rule haplotype_caller:
    input:
        # single or list of bam files
        bam="mapped/{sample}.bam",
        ref="genome.fasta"
        # known="dbsnp.vcf"  # optional
    output:
        gvcf="calls/{sample}.g.vcf",
    log:
        "logs/gatk/haplotypecaller/{sample}.log"
    params:
        extra="",  # optional
        java_opts="", # optional
    wrapper:
        "0.30.0/bio/gatk/haplotypecaller"

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.

Notes

Authors

  • Johannes Köster
  • Jake VanCampen

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"


import os

from snakemake.shell import shell

known = snakemake.input.get("known", "")
if known:
    known = "--dbsnp " + known

extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")
bams = snakemake.input.bam
if isinstance(bams, str):
    bams = [bams]
bams = list(map("-I {}".format, bams))

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell("gatk --java-options '{java_opts}' HaplotypeCaller {extra} "
      "-R {snakemake.input.ref} {bams} "
      "-ERC GVCF "
      "-O {snakemake.output.gvcf} {known} {log}")