#!/bin/bash -Ceuo pipefail
hard_filter_vcf.py \
--in-vcf positive_somatic_control_2.snv_indel.annotated.vcf.gz \
--tumor-sample-name 'Sig_18_tissue' \
--normal-sample-name 'reference-NA12878' \
--pon-vcf pon_tnseq_42_curated_v4.vcf.gz \
--pot-vcf aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz \
\
--out-vcf positive_somatic_control_2.snv_indel.filtered.vcf.gz
cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:HARD_FILTER_VCF":
python: $(python3 --version | sed 's/Python //')
END_VERSIONS