GATK APPLYVQSR¶
Run gatk ApplyVQSR.
URL:
Example¶
This wrapper can be used in the following way:
rule apply_vqsr:
input:
vcf="test.vcf",
recal="snps.recal",
tranches="snps.tranches",
ref="ref.fasta",
output:
vcf="test.snp_recal.vcf",
log:
"logs/gatk/applyvqsr.log",
params:
mode="SNP", # set mode, must be either SNP, INDEL or BOTH
extra="", # optional
resources:
mem_mb=50,
wrapper:
"v1.3.1/bio/gatk/applyvqsr"
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=4.2
snakemake-wrapper-utils=0.3
Input/Output¶
Input:
- VCF file
- Recalibration file
- Tranches file
Output:
- Variant QualityScore-Recalibrated VCF
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.
- For more information, see https://gatk.broadinstitute.org/hc/en-us/articles/360037226332-ApplyVQSR
Authors¶
- Brett Copeland
- Filipe G. Vieira
Code¶
__author__ = "Brett Copeland"
__copyright__ = "Copyright 2021, Brett Copeland"
__email__ = "brcopeland@ucsd.edu"
__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)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' ApplyVQSR"
" --variant {snakemake.input.vcf}"
" --recal-file {snakemake.input.recal}"
" --reference {snakemake.input.ref}"
" --tranches-file {snakemake.input.tranches}"
" --mode {snakemake.params.mode}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.vcf}"
" {log}"
)