.command.sh - Workdir - DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC (germline_control_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/390ac73ff372b56a0b4b9902b9d2bd/.command.sh
Size: 509 bytes
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC (germline_control_2)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools norm \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output germline_control_2.haplotyper.split.vcf.gz \
    -m - --output-type z --write-index=tbi \
    --threads 1 \
    germline_control_2.haplotyper.merged.vcf.gz

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