GATK VARIANTFILTRATION

Run gatk VariantFiltration.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570403488667-VariantFiltration

Example

This wrapper can be used in the following way:

rule gatk_filter:
    input:
        vcf="calls/snvs.vcf",
        ref="genome.fasta",
#        intervals="targets.bed",
    output:
        vcf="calls/snvs.filtered.vcf",
    log:
        "logs/gatk/filter/snvs.log",
    params:
        filters={"myfilter": "AB < 0.2 || MQ0 > 50"},
        extra="",  # optional arguments, see GATK docs
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0/bio/gatk/variantfiltration"

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

Authors

• Johannes Köster

• Jake VanCampen

• Filipe G. Vieira

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)


filters = [
    "--filter-name {} --filter-expression '{}'".format(name, expr.replace("'", "\\'"))
    for name, expr in snakemake.params.filters.items()
]


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}' VariantFiltration"
        " --variant {snakemake.input.vcf}"
        " --reference {snakemake.input.ref}"
        " {filters}"
        " {intervals}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output.vcf}"
        " {log}"
    )