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

mkdir GM24385_0001_RNA_0001_23H5VFLT4_s40

all_qc \
-bam "GM24385_0001_RNA_0001_23H5VFLT4_s40.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 GM24385_0001_RNA_0001_23H5VFLT4_s40 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders GM24385_0001_RNA_0001_23H5VFLT4_s40/* -output GM24385_0001_RNA_0001_23H5VFLT4_s40/GM24385_0001_RNA_0001_23H5VFLT4_s40_full_basic_stats.tsv

head -n1 GM24385_0001_RNA_0001_23H5VFLT4_s40/GM24385_0001_RNA_0001_23H5VFLT4_s40_full_basic_stats.tsv > GM24385_0001_RNA_0001_23H5VFLT4_s40/GM24385_0001_RNA_0001_23H5VFLT4_s40_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" GM24385_0001_RNA_0001_23H5VFLT4_s40/GM24385_0001_RNA_0001_23H5VFLT4_s40_full_basic_stats.tsv >> GM24385_0001_RNA_0001_23H5VFLT4_s40/GM24385_0001_RNA_0001_23H5VFLT4_s40_basic_stats.tsv