File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/84bfcd67eb73a6f356645a6da7b062/.command.sh
Size
497 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC (HCC1395_BL)
Attempt

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#!/bin/bash -Ceuo pipefail
bcftools norm \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output HCC1395_BL.haplotyper.split.vcf.gz \
    -m - --output-type z --write-index=tbi \
    --threads 6 \
    HCC1395_BL.haplotyper.merged.vcf.gz

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