#!/bin/bash -Ceuo pipefail
bcftools norm \
--fasta-ref Homo_sapiens_assembly38.fasta \
--output 1136_7L-N1-BDNA-1_A237CFYLT3_1.germline.normalized.vcf.gz \
-a -m -both --old-rec-tag OLD_VARIANT --output-type z --write-index=tbi \
--threads 6 \
1136_7L-N1-BDNA-1_A237CFYLT3_1.haplotyper_rf.gt_corrected.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_GERMLINE:BCFTOOLS_NORM":
bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS