GATK APPLYVQSR

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/gatk/applyvqsr?label=version%20update%20pull%20requests

Run gatk ApplyVQSR.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570419503259-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=1024,
    wrapper:
        "v3.8.0-1-g149ef14/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.

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

  • Recalibration file

  • Tranches file

Output:

  • Variant QualityScore-Recalibrated VCF

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}"
    )