#!/bin/bash -Ceuo pipefail
set -euo pipefail

gatk --java-options '-Xmx14g' Mutect2 \
    -R 'hg38.fa' \
    -I 'LS0882_tumor.bam' \
    --tumor-sample 'LS0882' \
    -L 'TST500C_manifest.bed' \
    -O 'LS0882.mutect2.raw.vcf.gz' \
    --native-pair-hmm-threads 4 \
    --max-mnp-distance 0 \
    --germline-resource 'af-only-gnomad.hg38.vcf.gz'

gatk --java-options '-Xmx14g' FilterMutectCalls \
    -R 'hg38.fa' \
    -V 'LS0882.mutect2.raw.vcf.gz' \
    --stats 'LS0882.mutect2.raw.vcf.gz.stats' \
    -O 'LS0882.mutect2.filtered.vcf.gz'

gatk --java-options '-Xmx14g' SelectVariants \
    -R 'hg38.fa' \
    -V 'LS0882.mutect2.filtered.vcf.gz' \
    --exclude-filtered true \
    -O 'LS0882.mutect2.pass.vcf.gz'