GATK GENOTYPEGVCFS

Run gatk GenotypeGVCFs.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570489472411-GenotypeGVCFs

Example

This wrapper can be used in the following way:

rule genotype_gvcfs:
    input:
        gvcf="calls/all.g.vcf",  # combined gvcf over multiple samples
    # N.B. gvcf or genomicsdb must be specified
    # in the latter case, this is a GenomicsDB data store
        ref="genome.fasta"
    output:
        vcf="calls/all.vcf",
    log:
        "logs/gatk/genotypegvcfs.log"
    params:
        extra="",  # optional
        java_opts="", # optional
    resources:
        mem_mb=1024
    wrapper:
        "v3.9.0-1-gc294552/bio/gatk/genotypegvcfs"

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 or GenomicsDB workspace

• reference genome

Output:

• VCF file with genotypes

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)

intervals = snakemake.input.get("intervals", "")
if not intervals:
    intervals = snakemake.params.get("intervals", "")
if intervals:
    intervals = "--intervals {}".format(intervals)

dbsnp = snakemake.input.get("known", "")
if dbsnp:
    dbsnp = "--dbsnp {}".format(dbsnp)

# Allow for either an input gvcf or GenomicsDB
gvcf = snakemake.input.get("gvcf", "")
genomicsdb = snakemake.input.get("genomicsdb", "")
if gvcf:
    if genomicsdb:
        raise Exception("Only input.gvcf or input.genomicsdb expected, got both.")
    input_string = gvcf
else:
    if genomicsdb:
        input_string = "gendb://{}".format(genomicsdb)
    else:
        raise Exception("Expected input.gvcf or input.genomicsdb.")

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


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' GenotypeGVCFs"
        " --variant {input_string}"
        " --reference {snakemake.input.ref}"
        " {dbsnp}"
        " {intervals}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output.vcf}"
        " {log}"
    )