mkdir -p BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed
seqtool depth -bam BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz
saturation_plot -bams BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_qc.tsv
fragment_size -bams BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output_prefix BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup && contamination -input BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/contamination.tsv
tabix -s 1 -b 2 -e 2 BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv
cat BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md -output BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.png
seqtool read_qc -bed Twist_rna_exome_AND_fusion_hg38.bed -n_threads 1 -bam_threads 2 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool reads_per_target -bed Twist_rna_exome_AND_fusion_hg38.bed -threads 1 -bam_threads 2 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz> BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/depth_stats.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool gc_bias -reference ref_genome.fa -bed Twist_rna_exome_AND_fusion_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv
cat BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/qc_complete.txt