GATK VARIANTEVAL

Run gatk VariantEval.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570243836187-VariantEval-BETA-

Example

This wrapper can be used in the following way:

rule gatk_varianteval:
    input:
        vcf="calls/snvs.vcf",
        ref="genome.fasta",
        dict="genome.dict",
        # comp="calls/comp.vcf", # optional comparison VCF
    output:
        vcf="snvs.varianteval.grp",
    log:
        "logs/gatk/varianteval/snvs.log",
    params:
        extra="",  # optional arguments, see GATK docs
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0/bio/gatk/varianteval"

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 files

• BAM/CRAM files (optional)

• reference genome (optional)

• reference dictionary (optional)

• vcf.gz of known variants (optional)

• PED (pedigree) file (optional)

Output:

• Evaluation tables detailing the results of the eval modules on VCF file

Authors

• Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, 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)


vcf = snakemake.input.vcf
if isinstance(vcf, str):
    vcf = "--eval  {}".format(vcf)
else:
    vcf = list(map("--eval {}".format, vcf))

bam = snakemake.input.get("bam", "")
if bam:
    if isinstance(bam, str):
        bam = "--input  {}".format(bam)
    else:
        bam = list(map("--input {}".format, bam))

ref = snakemake.input.get("ref", "")
if ref:
    ref = "--reference " + ref

ref_dict = snakemake.input.get("dict", "")
if ref_dict:
    ref_dict = "--sequence-dictionary " + ref_dict

known = snakemake.input.get("known", "")
if known:
    known = "--dbsnp " + known

comp = snakemake.input.get("comp", "")
if comp:
    if isinstance(comp, str):
        comp = "--comparison  {}".format(comp)
    else:
        comp = list(map("--comparison {}".format, comp))

ped = snakemake.input.get("ped", "")
if ped:
    ped = "--pedigree " + ped


log = snakemake.log_fmt_shell(stdout=True, stderr=True)


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' VariantEval"
        " {vcf}"
        " {bam}"
        " {ref}"
        " {ref_dict}"
        " {known}"
        " {ped}"
        " {comp}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " --output {snakemake.output[0]}"
        " {log}"
    )