#!/bin/bash -Ceuo pipefail
calculate_tmb_snv_indel.py \
    --in-vcf positive_somatic_control_2.snv_indel.filtered.vcf.gz \
    --in-bed xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed \
    --tumor-sample-name 'Sig_18_tissue' \
    --normal-sample-name 'reference-NA12878' \
    --threshold 10.0 \
    --min-tumor-vaf 0.05 \
    --min-tumor-dp 25 \
    --min-alt-reads 3 \
    --out-vcf positive_somatic_control_2.snv_indel.phased.vep.final.vcf.gz \
    --out-summary positive_somatic_control_2.snv_indel.tmb.txt \
    --out-csv positive_somatic_control_2.snv_indel.tmb.csv \
    --out-variants positive_somatic_control_2.snv_indel.tmb.vars.txt

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:TMB_SNV_INDEL":
    python: $(python3 --version | sed 's/Python //')
END_VERSIONS