.command.out - Workdir - DAQ:BAM_POSTDEDUP_QC:SEQTOOL (FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/852703caa305c4a6f1cbb4472f2ff9/.command.out
Size: 19.1 KB
Task: DAQ:BAM_POSTDEDUP_QC:SEQTOOL (FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1)
Attempt
Content

mkdir -p FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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 > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/full_bed.bed


saturation_plot       -bams FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam       -region chr20       -output FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/saturation_plot.png       -threads 1 
seqtool depth -bam FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam -bed FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/saturation_qc.tsv 
fragment_size       -bams FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam       -region chr20       -output_prefix FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/fragsize       -threads 1 
samtools mpileup   -B --min-MQ 60 --min-BQ 30    -f Homo_sapiens_assembly38.fasta   -l dbsnp_hg38_contam_sites.bed   FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.mpileup && contamination -input FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/contamination.tsv 
seqtool noise   -bam FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam   -ref Homo_sapiens_assembly38.fasta   -region chr20   -include_bed FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/full_bed.bed   -exclude_bed dbsnp138_hg38_common.bed   -threads 1 > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.noise_summary.tsv 










tabix -s 1 -b 2 -e 2 FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz


seqtool depth_hist     -nbins 500     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz     > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth_hist.tsv


cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md         -output FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/reads_per_target.altera_v3_targets_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed altera_v3_targets_postQC_hg38.bed  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/reads_per_target.altera_v3_targets_coding_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed altera_v3_targets_coding_postQC_hg38.bed  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/reads_per_target.altera_v3_targets_noncoding_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed altera_v3_targets_noncoding_postQC_hg38.bed  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/reads_per_target.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv 
seqtool depth_stats  -bed FINAL_hotspot_list_07302025_hg38_sorted.bed  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/read_qc.foresight_clarity_targets_hg38.bed.tsv
seqtool reads_per_target     -bed foresight_clarity_targets_hg38.bed     -threads 1     -bam_threads 2     FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/reads_per_target.foresight_clarity_targets_hg38.bed.tsv 
seqtool depth_stats  -bed foresight_clarity_targets_hg38.bed  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.depth.gz> FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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  FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam  > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv 


















cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias.FINAL_hotspot_list_07302025_hg38_sorted.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias.foresight_clarity_targets_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_coding_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 




cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_noncoding_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 








cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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 "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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 FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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 "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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" 




cat FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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 "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed" -output "FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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" 






















echo `date` > FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md/qc_complete.txt