GATK HAPLOTYPECALLER

Run gatk HaplotypeCaller.

URL:

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",
    #       bam="{sample}.assemb_haplo.bam",
    log:
        "logs/gatk/haplotypecaller/{sample}.log",
    params:
        extra="",  # optional
        java_opts="",  # optional
    threads: 4
    resources:
        mem_mb=1024,
    wrapper:
        "v1.1.0/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.

Software dependencies

• gatk4=4.2
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• bam file

Output:

• GVCF file

Notes

• The 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).
• The extra param allows for additional program arguments.
• For more information see, https://gatk.broadinstitute.org/hc/en-us/articles/4405451272731-HaplotypeCaller

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
from snakemake_wrapper_utils.java import get_java_opts

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

bam_output = snakemake.output.get("bam", "")
if bam_output:
    bam_output = "--bam-output " + str(bam_output)

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

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} "
    "--native-pair-hmm-threads {snakemake.threads} "
    "-R {snakemake.input.ref} {bams} "
    "-ERC GVCF {bam_output} "
    "-O {snakemake.output.gvcf} {known} {log}"
)