File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/b7238b41f85f99fd21b74a6eb6ee99/.command.sh
Size
565 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:CONCAT_WHATSHAP_VCFS (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
tabix HCC1395_tumor_vs_HCC1395_BL.snv_indel.whatshap.chr21.phased.vcf.gz

bcftools concat \
    --output HCC1395_tumor_vs_HCC1395_BL.snv_indel.phased.vcf.gz \
    --allow-overlaps --output-type z --write-index=tbi \
    --threads 6 \
    HCC1395_tumor_vs_HCC1395_BL.snv_indel.whatshap.chr21.phased.vcf.gz

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