GATK VARIANTFILTRATION

Run gatk VariantFiltration.

Software dependencies

• gatk4 ==4.0.5.1

Example

This wrapper can be used in the following way:

rule gatk_filter:
    input:
        vcf="calls/snvs.vcf",
        ref="genome.fasta",
    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
    wrapper:
        "0.30.0/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. “-Xmx4G” for one, and “-Xmx4G -XX:ParallelGCThreads=10” for two options.
• The extra param alllows for additional program arguments.
• For more inforamtion see, https://software.broadinstitute.org/gatk/documentation/article?id=11050

Authors

• Johannes Köster
• Jake VanCampen

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"


from snakemake.shell import shell

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

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell("gatk --java-options '{java_opts}' VariantFiltration -R {snakemake.input.ref} -V {snakemake.input.vcf} "
      "{extra} {filters} -O {snakemake.output.vcf} {log}")