GATK VARIANTSTOTABLE

Run gatk VariantsToTable

URL: https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable

Example

This wrapper can be used in the following way:

rule gatk_variantstotable:
    input:
        vcf="calls/snvs.vcf",
#        intervals="intervals.bed",
    output:
        tab="calls/snvs.tab",
    log:
        "logs/gatk/varintstotable.log",
    params:
        extra="-F CHROM -F POS -F TYPE -GF AD",
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.0.2/bio/gatk/variantstotable"

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=4.4.0.0

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• A VCF file to convert to a table

Output:

• A tab-delimited file containing the values of the requested fields in the VCF file

Authors

• Dmitry Bespiatykh

Code

"""Snakemake wrapper for GATK VariantsToTable"""

__author__ = "Dmitry Bespiatykh"
__copyright__ = "Copyright 2023, Dmitry Bespiatykh"
__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)


intervals = snakemake.input.get("intervals", "")
if not intervals:
    intervals = snakemake.params.get("intervals", "")
if intervals:
    intervals = "--intervals {}".format(intervals)


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' VariantsToTable"
        " --variant {snakemake.input.vcf}"
        " {intervals}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output.tab}"
        " {log}"
    )