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

mkdir NTC_0001_0001_23H5VFLT4_s15

all_qc \
-bam "NTC_0001_0001_23H5VFLT4_s15.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 NTC_0001_0001_23H5VFLT4_s15 \
-reference "ref_genome.fa" \
-region 'chr20'

merge_qc -folders NTC_0001_0001_23H5VFLT4_s15/* -output NTC_0001_0001_23H5VFLT4_s15/NTC_0001_0001_23H5VFLT4_s15_full_basic_stats.tsv

head -n1 NTC_0001_0001_23H5VFLT4_s15/NTC_0001_0001_23H5VFLT4_s15_full_basic_stats.tsv > NTC_0001_0001_23H5VFLT4_s15/NTC_0001_0001_23H5VFLT4_s15_basic_stats.tsv
grep -e "$(basename Twist_rna_exome_AND_fusion_hg38.bed)" NTC_0001_0001_23H5VFLT4_s15/NTC_0001_0001_23H5VFLT4_s15_full_basic_stats.tsv >> NTC_0001_0001_23H5VFLT4_s15/NTC_0001_0001_23H5VFLT4_s15_basic_stats.tsv