GATK VARIANTEVAL

Run gatk VariantEval.

URL:

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:
        "v1.2.0/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.

Software dependencies

  • gatk4=4.2
  • snakemake-wrapper-utils=0.3

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

Notes

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}"
    )