#!/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