.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY (Sig_18_Blood)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/ff12074409b5b9339f249918690a02/.command.sh
Size: 458 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY (Sig_18_Blood)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools query \
     \
     \
     \
    -i 'TYPE="indel"' -f '%CHROM\t%POS0\t%END\n' \
    Sig_18_Blood.haplotyper.split.vcf.gz \
    > Sig_18_Blood.bed

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS