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

mkdir rna_s1221_S42

all_qc \
-bam "rna_s1221_S42.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 rna_s1221_S42 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders rna_s1221_S42/* -output rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv

head -n1 rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv > rna_s1221_S42/rna_s1221_S42_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv >> rna_s1221_S42/rna_s1221_S42_basic_stats.tsv