#!/bin/bash -Ceuo pipefail
bcftools norm \
-a -m -both \
-f Homo_sapiens_assembly38.fasta \
HCC1395_BL.tumor_genotyped.vcf.gz \
-Oz -o tumor_norm.vcf.gz
bcftools index -t tumor_norm.vcf.gz
transfer_caller_ad.py \
--vcf HCC1395_BL.prefiltered.vcf.gz \
--tumor-vcf tumor_norm.vcf.gz \
--output HCC1395_BL.readcount_annotated.vcf.gz
tabix -p vcf HCC1395_BL.readcount_annotated.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:TRANSFER_CALLER_AD":
bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*//')
cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
END_VERSIONS