.command.out - Workdir - DAQ:BAM_POSTDEDUP_QC:SEQTOOL (HCC1395_tumor)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/950a12fc155442dc354ac91f8ce010/.command.out
Size: 14.4 KB
Task: DAQ:BAM_POSTDEDUP_QC:SEQTOOL (HCC1395_tumor)
Attempt
Content

mkdir -p HCC1395_tumor/HCC1395_tumor.md/


cat xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed altera_v3_targets_postQC_hg38.bed altera_v3_targets_coding_postQC_hg38.bed altera_v3_targets_noncoding_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed FINAL_hotspot_list_07302025_hg38_sorted.bed foresight_clarity_targets_hg38.bed | cut -f 1-3 | bedtools sort -g Homo_sapiens_assembly38.fasta.fai | bedtools merge > HCC1395_tumor/HCC1395_tumor.md/full_bed.bed


seqtool depth -bam HCC1395_tumor.md.bam -bed HCC1395_tumor/HCC1395_tumor.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz
saturation_plot       -bams HCC1395_tumor.md.bam       -region chr20       -output HCC1395_tumor/HCC1395_tumor.md/saturation_plot.png       -threads 1 
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/saturation_qc.tsv 
fragment_size       -bams HCC1395_tumor.md.bam       -region chr20       -output_prefix HCC1395_tumor/HCC1395_tumor.md/fragsize       -threads 1 
samtools mpileup   -B --min-MQ 60 --min-BQ 30    -f Homo_sapiens_assembly38.fasta   -l dbsnp_hg38_contam_sites.bed   HCC1395_tumor.md.bam > HCC1395_tumor.md.mpileup && contamination -input HCC1395_tumor.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > HCC1395_tumor/HCC1395_tumor.md/contamination.tsv 
seqtool noise   -bam HCC1395_tumor.md.bam   -ref Homo_sapiens_assembly38.fasta   -region chr20   -include_bed HCC1395_tumor/HCC1395_tumor.md/full_bed.bed   -exclude_bed dbsnp138_hg38_common.bed   -threads 1 > HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.noise_summary.tsv 












tabix -s 1 -b 2 -e 2 HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz


seqtool depth_hist     -nbins 500     HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz     > HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth_hist.tsv


cat HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title HCC1395_tumor.md         -output HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.png


seqtool read_qc    -bed xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv
seqtool reads_per_target     -bed xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv 
seqtool depth_stats  -bed xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv 
seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv 
seqtool read_qc    -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv
seqtool reads_per_target     -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv 
seqtool depth_stats  -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv 
seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv 
seqtool read_qc    -bed altera_v3_targets_postQC_hg38.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.altera_v3_targets_postQC_hg38.bed.tsv
seqtool reads_per_target     -bed altera_v3_targets_postQC_hg38.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.altera_v3_targets_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed altera_v3_targets_postQC_hg38.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.altera_v3_targets_postQC_hg38.bed.tsv 
seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed altera_v3_targets_postQC_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.altera_v3_targets_postQC_hg38.bed.tsv 
seqtool read_qc    -bed altera_v3_targets_coding_postQC_hg38.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv
seqtool reads_per_target     -bed altera_v3_targets_coding_postQC_hg38.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.altera_v3_targets_coding_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed altera_v3_targets_coding_postQC_hg38.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.altera_v3_targets_coding_postQC_hg38.bed.tsv 
seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed altera_v3_targets_coding_postQC_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv 
seqtool read_qc    -bed altera_v3_targets_noncoding_postQC_hg38.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv
seqtool reads_per_target     -bed altera_v3_targets_noncoding_postQC_hg38.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.altera_v3_targets_noncoding_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed altera_v3_targets_noncoding_postQC_hg38.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.altera_v3_targets_noncoding_postQC_hg38.bed.tsv 
seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed altera_v3_targets_noncoding_postQC_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv 
seqtool read_qc    -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv
seqtool reads_per_target     -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv 
seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv 
seqtool read_qc    -bed FINAL_hotspot_list_07302025_hg38_sorted.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv
seqtool reads_per_target     -bed FINAL_hotspot_list_07302025_hg38_sorted.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv 
seqtool depth_stats  -bed FINAL_hotspot_list_07302025_hg38_sorted.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv 
seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed FINAL_hotspot_list_07302025_hg38_sorted.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv 
seqtool read_qc    -bed foresight_clarity_targets_hg38.bed     -n_threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/read_qc.foresight_clarity_targets_hg38.bed.tsv
seqtool reads_per_target     -bed foresight_clarity_targets_hg38.bed     -threads 1     -bam_threads 2     HCC1395_tumor.md.bam > HCC1395_tumor/HCC1395_tumor.md/reads_per_target.foresight_clarity_targets_hg38.bed.tsv 
seqtool depth_stats  -bed foresight_clarity_targets_hg38.bed  HCC1395_tumor/HCC1395_tumor.md/HCC1395_tumor.md.depth.gz> HCC1395_tumor/HCC1395_tumor.md/depth_stats.foresight_clarity_targets_hg38.bed.tsv 


seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed foresight_clarity_targets_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  HCC1395_tumor.md.bam  > HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv 






cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.FINAL_hotspot_list_07302025_hg38_sorted.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 




cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.altera_v3_targets_coding_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 


cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.altera_v3_targets_noncoding_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 




cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.altera_v3_targets_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 












cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.foresight_clarity_targets_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 










cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 








cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 








cat HCC1395_tumor/HCC1395_tumor.md/gc_bias_qc.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "HCC1395_tumor.md" -suptitle "xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed" -output "HCC1395_tumor/HCC1395_tumor.md/gc_bias.xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 
























echo `date` > HCC1395_tumor/HCC1395_tumor.md/qc_complete.txt