.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE (Sig_18_Blood;germline_cnv)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/81d628dfc903142c0be59ae02b3b2d/.command.sh
Size: 527 bytes
Task: NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE (Sig_18_Blood;germline_cnv)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools index Sig_18_Blood.vcf.gz

bcftools \
    annotate \
    --output-type z --write-index=tbi -c CHROM,FROM,TO,RPMCat \
    --annotations repeatmasker_grch38.bed.gz \
    --header-lines repeatmasker_header.txt \
    --output Sig_18_Blood_RPM.vcf.gz \
    --threads 1 \
    Sig_18_Blood.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE":
    bcftools: $( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS