#!/bin/bash -euo pipefail
pip install --quiet pyliftover
process_variants.py \
--vcf 1029_BC0-T1-TDNA-1_A23MCTVLT4_1_vs_1029_BC0-N1-BDNA-1_B23KFG5LT4_1.snv_indel.phased.vep.final.vcf.gz \
--specimen "1029_BC0" \
--chain hg38ToHg19.over.chain.gz \
--pon pon_tnseq_42_curated_v4.vcf.gz \
--pot aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz \
--output "1029_BC0.csv"
cat <<-END_VERSIONS > versions.yml
"PROCESS_VARIANTS":
pysam: $(python3 -c "import pysam; print(pysam.__version__)")
pyliftover: $(python3 -c "import pyliftover; print(pyliftover.__version__)")
END_VERSIONS