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

mkdir rna_s1200_S21

all_qc \
-bam "rna_s1200_S21.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_s1200_S21 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders rna_s1200_S21/* -output rna_s1200_S21/rna_s1200_S21_full_basic_stats.tsv

head -n1 rna_s1200_S21/rna_s1200_S21_full_basic_stats.tsv > rna_s1200_S21/rna_s1200_S21_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" rna_s1200_S21/rna_s1200_S21_full_basic_stats.tsv >> rna_s1200_S21/rna_s1200_S21_basic_stats.tsv