.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/3ae57aa98a01274135ce72c56bc45c/.command.out
Size: 4.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1)
Attempt
Content

mkdir -p BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/


cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/full_bed.bed


seqtool depth -bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam -bed BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz
saturation_plot       -bams BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam       -region chr20       -output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/saturation_plot.png       -threads 1 
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/saturation_qc.tsv 
fragment_size       -bams BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam       -region chr20       -output_prefix BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_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   BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.mpileup && contamination -input BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/contamination.tsv 








tabix -s 1 -b 2 -e 2 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz


seqtool depth_hist     -nbins 500     BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz     > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv


cat BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md         -output BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.png




seqtool read_qc    -bed Twist_rna_exome_AND_fusion_hg38.bed     -n_threads 1     -bam_threads 2     BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_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     BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_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  BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.depth.gz> BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_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  BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam  > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv 








cat BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 


echo `date` > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md/qc_complete.txt