#!/bin/bash -Ceuo pipefail
score_chip_variants.py \
--vcf 1136_6I8-N1-BDNA-1_B23MHTGLT4_1.readcount_annotated.vcf.gz \
--output 1136_6I8-N1-BDNA-1_B23MHTGLT4_1.scored.vcf.gz \
--blacklist cohort_blacklist.bed.gz \
--cosmic-heme cosmic_heme.tsv.gz \
--gene-tiers gene_tiers.tsv
tabix -p vcf 1136_6I8-N1-BDNA-1_B23MHTGLT4_1.scored.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS":
score_chip_variants: $(score_chip_variants.py --version 2>&1 || echo "1.0.0")
cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
END_VERSIONS