GATK SELECTVARIANTS
Run gatk SelectVariants.
URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570332289307-SelectVariants
Example
This wrapper can be used in the following way:
rule gatk_select:
input:
vcf="calls/all.vcf",
ref="genome.fasta",
output:
vcf="calls/snvs.vcf",
log:
"logs/gatk/select/snvs.log",
params:
extra="--select-type-to-include SNP", # optional filter arguments, see GATK docs
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"v3.9.0/bio/gatk/selectvariants"
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:
vcf file
reference genome
Output:
filtered vcf file
Code
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
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)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' SelectVariants"
" --variant {snakemake.input.vcf}"
" --reference {snakemake.input.ref}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.vcf}"
" {log}"
)