GATK COMBINEGVCFS

Run gatk CombineGVCFs.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570423318427-CombineGVCFs

Example

This wrapper can be used in the following way:

rule genotype_gvcfs:
    input:
        gvcfs=["calls/a.g.vcf", "calls/b.g.vcf"],
        ref="genome.fasta",
    output:
        gvcf="calls/all.g.vcf",
    log:
        "logs/gatk/combinegvcfs.log",
    params:
        extra="",  # optional
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0-49-g6f33607/bio/gatk/combinegvcfs"

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

• 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.

Software dependencies

• gatk4=4.5.0.0

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• GVCF files of multiple samples

Output:

• Combined GVCF

Authors

• Johannes Köster

• Jake VanCampen

• Filipe G. Vieira

Code

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


import os
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)

gvcfs = list(map("--variant {}".format, snakemake.input.gvcfs))

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

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' CombineGVCFs"
        " {gvcfs}"
        " --reference {snakemake.input.ref}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output.gvcf}"
        " {log}"
    )