.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC (Sig_18_Blood)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/cfa271c1619a2471cc935615b4f364/.command.sh
Size: 501 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SPLIT_MULTIALLELIC (Sig_18_Blood)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools norm \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output Sig_18_Blood.haplotyper.split.vcf.gz \
    -m - --output-type z --write-index=tbi \
    --threads 6 \
    Sig_18_Blood.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