.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (Sig_18_Blood;sentieon_haplotyper_rf)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/46f60ea74e988d4ea85068425474e5/.command.sh
Size: 368 bytes
Task: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (Sig_18_Blood;sentieon_haplotyper_rf)
Attempt

Content

#!/bin/bash -Ceuo pipefail
vcftools \
    --gzvcf Sig_18_Blood.deconflicted_germline.vcf.gz \
    --out Sig_18_Blood.deconflicted_germline \
    --TsTv-by-qual \
     \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL":
    vcftools: $(echo $(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
END_VERSIONS