GATK APPLYVQSR¶
Run gatk ApplyVQSR.
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:
"0.74.0/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==4.2.0.0
snakemake-wrapper-utils==0.1.3
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. “-Xmx4G” for one, and “-Xmx4G -XX:ParallelGCThreads=10” for two options.
- 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
Code¶
__author__ = "Brett Copeland"
__copyright__ = "Copyright 2021, Brett Copeland"
__email__ = "brcopeland@ucsd.edu"
__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)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"gatk --java-options '{java_opts}' ApplyVQSR {extra} "
"-R {snakemake.input.ref} -V {snakemake.input.vcf} "
"--recal-file {snakemake.input.recal} "
"--tranches-file {snakemake.input.tranches} "
"-mode {snakemake.params.mode} "
"--output {snakemake.output.vcf} "
"{log}"
)