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

mkdir PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1

all_qc \
-bam "PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1.md.bam" \
-beds Twist_rna_exome_AND_fusion_hg38.bed \
-dbsnp_vcf "Homo_sapiens_assembly38.dbsnp138.vcf.gz" \
-contamination_bed "dbsnp_hg38_contam_sites.bed" \
-output_folder PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1/* -output PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1/PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_full_basic_stats.tsv

head -n1 PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1/PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_full_basic_stats.tsv > PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1/PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1/PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_full_basic_stats.tsv >> PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1/PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_basic_stats.tsv