GATK COMBINEGVCFS

Run gatk CombineGVCFs.

URL:

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
    # 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
    wrapper:
        "v1.1.0/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.

Software dependencies

• gatk4==4.1.4.1
• snakemake-wrapper-utils==0.1.3

Input/Output

Input:

• GVCF files of multiple samples

Output:

• Combined GVCF

Notes

• The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-Xmx4G” for one, and “-Xmx4G -XX:ParallelGCThreads=10” for two options.
• The extra param allows for additional program arguments.
• For more information see, https://software.broadinstitute.org/gatk/documentation/article?id=11050

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


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

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

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