File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/7bd1154c42c0feecbb6302b488d8c8/.command.sh
Size
558 bytes
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS (negative_somatic_control_2)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
tabix negative_somatic_control_2.snv_indel.whatshap.chr21.phased.vcf.gz

bcftools concat \
    --output negative_somatic_control_2.snv_indel.phased.vcf.gz \
    --allow-overlaps --output-type z --write-index=tbi \
    --threads 1 \
    negative_somatic_control_2.snv_indel.whatshap.chr21.phased.vcf.gz

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS