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

mkdir BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3

all_qc \
-bam "BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/* -output BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_full_basic_stats.tsv

head -n1 BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_full_basic_stats.tsv > BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_full_basic_stats.tsv >> BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3_basic_stats.tsv