File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/7b99caa13d9033ee3cdb689c8a093a/.command.sh
Size
466 bytes
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:BCFTOOLS_QUERY (germline_control_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
bcftools query \
     \
     \
     \
    -i 'TYPE="indel"' -f '%CHROM\t%POS0\t%END\n' \
    germline_control_1.haplotyper.split.vcf.gz \
    > germline_control_1.bed

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC: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