gatk gatk genotypegvcfs

gatk genotypegvcfs

Version:
4.1.4.1
Identifier: TL_55f722_ec.3a
Tool
1__author__ = "Johannes Köster"
2__copyright__ = "Copyright 2018, Johannes Köster"
3__email__ = "johannes.koester@protonmail.com"
4__license__ = "MIT"
5
6
7import os
8
9from snakemake.shell import shell
10from snakemake_wrapper_utils.java import get_java_opts
11
12
13extra = snakemake.params.get("extra", "")
14java_opts = get_java_opts(snakemake)
15
16log = snakemake.log_fmt_shell(stdout=True, stderr=True)
17shell(
18    "gatk --java-options '{java_opts}' GenotypeGVCFs {extra} "
19    "-V {snakemake.input.gvcf} "
20    "-R {snakemake.input.ref} "
21    "-O {snakemake.output.vcf} {log}"
22)
23