#!/bin/bash -Ceuo pipefail
calculate_tmb.py \
--in-bed xgen-exome-hyb-panel-v2-targets-hg38_short.mrg_chr21.bed \
--in-vcf custom_Sig_18_tumor_normal.tnseq.filtered_snpEff.ann.vcf.gz \
--threshold 10.0 \
--tumor-sample-name 'Sig_18_tissue' \
--normal-sample-name 'Sig_18_Blood' \
--ignore-high-ploidy \
--filter-for-pass \
--filter-for-biallelic \
--min-tumor-vaf 0.05 \
--out-summary-file custom_Sig_18_tumor_normal.tnseq.filtered_snpEff.ann.tmb.txt \
--out-tmb-summary-csv custom_Sig_18_tumor_normal.tnseq.filtered_snpEff.ann.tmb.csv \
--out-variant-list-file custom_Sig_18_tumor_normal.tnseq.filtered_snpEff.ann.vars.txt