GATK VARIANTANNOTATOR

Run gatk VariantAnnotator.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570271608219-VariantAnnotator

Example

This wrapper can be used in the following way:

rule gatk_annotator:
    input:
        vcf="calls/snvs.vcf.gz",
        aln="mapped/a.bam",
        bai="mapped/a.bam.bai",
        ref="genome.fasta",
        db="calls/snvs.vcf.gz",
#        intervals="targets.bed",
    output:
        vcf="snvs.annot.vcf",
    log:
        "logs/gatk/annotator/snvs.log",
    params:
        extra="--resource-allele-concordance -A Coverage --expression db.END",
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.9.0-14-g476823b/bio/gatk/variantannotator"

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

• BAM file

• reference genome

• VCF of known variation

Output:

• annotated VCF file

Authors

• Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__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)


input = snakemake.input.get("aln", "")
if input:
    input = f"--input {input}"

reference = snakemake.input.get("ref", "")
if reference:
    reference = f"--reference {reference}"

dbsnp = snakemake.input.get("known", "")
if dbsnp:
    dbsnp = f"--dbsnp {dbsnp}"

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

resources = [
    f"--resource:{name} {file}"
    for name, file in snakemake.input.items()
    if name not in ["vcf", "aln", "ref", "known", "intervals", "bai"]
]


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