#!/bin/bash -Ceuo pipefail
bcftools norm \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output 1136_6I8-N1-BDNA-1_B23MHTGLT4_1.chip.normalized.vcf.gz \
    -a -m -both --old-rec-tag OLD_VARIANT --output-type z --write-index=tbi \
    --threads 6 \
    1136_6I8-N1-BDNA-1_B23MHTGLT4_1.tnseq_tumor_only.filtered_snpEff.ann.vcf.gz

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