.command.log - Workdir - DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1136_4GR-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/eed0f49f654c65e408c87deac6af17/.command.log
Size: 33.3 KB
Task: DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1136_4GR-T1-TDNA-1_A23MHWWLT4_1)
Attempt
Content

  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/foresight_clarity_targets_hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/eed0f49f654c65e408c87deac6af17/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/FINAL_hotspot_list_07302025_hg38_sorted.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/456c7297230f9d5b53e61a8b972390/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/456c7297230f9d5b53e61a8b972390/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-platform-sandbox/platform-users/ralla/nfcore_rnafusion_resources/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/eed0f49f654c65e408c87deac6af17/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/dbsnp138_hg38_common.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed
==> STAGING COMPLETE (18 inputs)

mkdir -p 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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 > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed


seqtool depth -bam 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam -bed 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz
saturation_plot       -bams 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam       -region chr20       -output 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/saturation_plot.png       -threads 1 
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/saturation_qc.tsv 
fragment_size       -bams 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam       -region chr20       -output_prefix 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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   1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.mpileup && contamination -input 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/contamination.tsv 
seqtool noise   -bam 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam   -ref Homo_sapiens_assembly38.fasta   -region chr20   -include_bed 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed   -exclude_bed dbsnp138_hg38_common.bed   -threads 1 > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.noise_summary.tsv 
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[mpileup] 1 samples in 1 input files
loading BEDs...
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai

0it [00:00, ?it/s]
150488it [00:00, 1504841.97it/s][W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai

312662it [00:00, 1573579.20it/s]
477681it [00:00, 1608540.48it/s]
642570it [00:00, 1624455.08it/s]
808577it [00:00, 1637284.36it/s]
975149it [00:00, 1646932.85it/s]
1143937it [00:00, 1660148.90it/s]
1313299it [00:00, 1670792.72it/s]
1480379it [00:00, 1661249.68it/s]
1648716it [00:01, 1668043.30it/s]
1815532it [00:01, 1637670.66it/s]
1979420it [00:01, 1624609.84it/s]
2141971it [00:01, 1622574.55it/s]
2304289it [00:01, 1567941.41it/s]
2461465it [00:01, 1562460.79it/s]
2629689it [00:01, 1597450.62it/s]
2798021it [00:01, 1622694.68it/s]
2960525it [00:01, 1618500.82it/s]
3122537it [00:01, 1610195.66it/s]
3283671it [00:02, 1539760.29it/s]
3438317it [00:02, 1527306.89it/s]
3592319it [00:02, 1530980.74it/s]
3757273it [00:02, 1565687.95it/s]
3920391it [00:02, 1584992.58it/s]
4079144it [00:02, 1576110.69it/s]
4239246it [00:02, 1583478.78it/s]
4404645it [00:02, 1604279.55it/s]
4567968it [00:02, 1612899.17it/s]
4729343it [00:02, 1540763.74it/s]
4884398it [00:03, 1543490.05it/s]
5045591it [00:03, 1563389.58it/s]
5204581it [00:03, 1571194.14it/s]
5368711it [00:03, 1591911.24it/s]
5528138it [00:03, 1590357.89it/s]
5690499it [00:03, 1600116.80it/s]
5855758it [00:03, 1615768.60it/s]
6021137it [00:03, 1627005.35it/s]
6183907it [00:03, 1521384.45it/s]
6337467it [00:04, 1450072.23it/s]
6483933it [00:04, 1440008.25it/s]
6647895it [00:04, 1496549.70it/s]
6815970it [00:04, 1549460.15it/s]
6988157it [00:04, 1599718.15it/s]
7159767it [00:04, 1633929.15it/s]
7328332it [00:04, 1649131.02it/s]
7497313it [00:04, 1661202.86it/s]
7666213it [00:04, 1669473.92it/s]
7834647it [00:04, 1673892.24it/s]
8002206it [00:05, 1672889.47it/s]
8171395it [00:05, 1678564.45it/s]
8342130it [00:05, 1687173.81it/s]
8512287it [00:05, 1691478.25it/s]
8681479it [00:05, 1688148.14it/s]
8852541it [00:05, 1694863.47it/s]
9025406it [00:05, 1704973.52it/s]
9195922it [00:05, 1695984.08it/s]
9368754it [00:05, 1705627.43it/s]
9540737it [00:05, 1709690.03it/s]
9711722it [00:06, 1704001.19it/s]
9882136it [00:06, 1704014.02it/s]
10052853it [00:06, 1704923.41it/s]
10223353it [00:06, 1696085.27it/s]
10392976it [00:06, 1688261.62it/s]
10561987it [00:06, 1688802.07it/s]
10730878it [00:06, 1674117.96it/s]
10898320it [00:06, 1669072.35it/s]
11066698it [00:06, 1673308.85it/s]done loading BEDs.

11234481it [00:06, 1674584.64it/s]
11404237it [00:07, 1681294.27it/s]
11572379it [00:07, 1669426.73it/s]
11741731it [00:07, 1676592.74it/s]
11913238it [00:07, 1688068.78it/s]
12083951it [00:07, 1693754.18it/s]
12253344it [00:07, 1693609.11it/s]
12422717it [00:07, 1692753.88it/s]
12592912it [00:07, 1695497.78it/s]
12762478it [00:07, 1695476.62it/s]
12932030it [00:07, 1694494.68it/s]
13101483it [00:08, 1687580.55it/s]
13270250it [00:08, 1686325.39it/s]
13440939it [00:08, 1692430.73it/s]
13612616it [00:08, 1699706.46it/s]
13783157it [00:08, 1701404.50it/s]
13953302it [00:08, 1686062.41it/s]
14121942it [00:08, 1678033.43it/s]
14290007it [00:08, 1678676.60it/s]
14459518it [00:08, 1683447.53it/s]
14629454it [00:08, 1688190.91it/s]
14799823it [00:09, 1692815.36it/s]
14969116it [00:09, 1613479.67it/s]
15137150it [00:09, 1632684.24it/s]
15308287it [00:09, 1655697.77it/s]
15477816it [00:09, 1667309.89it/s]
15644909it [00:09, 1667797.48it/s]
15816152it [00:09, 1681057.34it/s]
15984447it [00:09, 1649110.93it/s]
16155764it [00:09, 1667972.72it/s]
16326253it [00:09, 1678811.31it/s]
16497205it [00:10, 1687927.93it/s]
16669183it [00:10, 1697360.26it/s]
16839010it [00:10, 1694890.32it/s]
17010069it [00:10, 1699567.49it/s]
17181287it [00:10, 1703328.36it/s]
17352977it [00:10, 1707380.89it/s]
17523740it [00:10, 1699558.75it/s]
17693721it [00:10, 1673247.76it/s]
17861145it [00:10, 1659020.28it/s]
18031299it [00:10, 1671519.60it/s]
18198526it [00:11, 1659832.75it/s]
18368518it [00:11, 1671694.78it/s]
18538902it [00:11, 1681241.29it/s]
18709921it [00:11, 1689860.66it/s]
18878947it [00:11, 1686314.39it/s]
19049060it [00:11, 1690730.56it/s]
19218155it [00:11, 1685363.24it/s]
19386709it [00:11, 1682584.36it/s]
19554980it [00:11, 1652266.94it/s]
19723943it [00:11, 1663259.13it/s]
19892426it [00:12, 1669561.19it/s]
20062714it [00:12, 1679467.25it/s]
20231647it [00:12, 1682401.93it/s]
20400447it [00:12, 1684065.76it/s]
20570688it [00:12, 1689544.99it/s]
20739667it [00:12, 1688566.47it/s]
20908541it [00:12, 1683333.01it/s]
21077881it [00:12, 1686328.81it/s]
21248795it [00:12, 1693136.85it/s]
21419190it [00:12, 1696350.34it/s]
21588833it [00:13, 1692458.45it/s]
21758086it [00:13, 1675838.43it/s]
21925708it [00:13, 1674798.05it/s]
22093294it [00:13, 1674990.06it/s]
22261381it [00:13, 1676733.22it/s]
22429167it [00:13, 1676966.62it/s]
22596874it [00:13, 1668414.01it/s]
22763731it [00:13, 1663845.11it/s]
22933159it [00:13, 1672911.95it/s]
23104544it [00:13, 1685134.86it/s]
23274663it [00:14, 1689924.16it/s]
23446125it [00:14, 1697306.94it/s]
23615960it [00:14, 1697604.16it/s]
23785727it [00:14, 1694351.76it/s]
23955223it [00:14, 1694519.84it/s][W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai

24124679it [00:14, 1685745.37it/s]
24293266it [00:14, 1626644.45it/s]
24462966it [00:14, 1647146.53it/s]
24634749it [00:14, 1667918.52it/s]
24806272it [00:14, 1681901.59it/s]
24974689it [00:15, 1655152.21it/s]
25140437it [00:15, 1539518.49it/s]
25307521it [00:15, 1576430.44it/s]
25476020it [00:15, 1607527.96it/s]
25642884it [00:15, 1625179.56it/s]
25807196it [00:15, 1630427.43it/s]
25975353it [00:15, 1645513.51it/s]
26140826it [00:15, 1648236.41it/s]
26310703it [00:15, 1663263.93it/s]
26479873it [00:16, 1671605.56it/s]
26649940it [00:16, 1680276.82it/s]
26818089it [00:16, 1677929.40it/s]
26987595it [00:16, 1682981.34it/s]
27160393it [00:16, 1696436.36it/s]
27331820it [00:16, 1701765.40it/s]
27502030it [00:16, 1685386.86it/s]
27670627it [00:16, 1684282.86it/s]
27839095it [00:16, 1645154.39it/s]
28005122it [00:16, 1649499.64it/s]
28175971it [00:17, 1666904.92it/s]
28346864it [00:17, 1679370.31it/s]
28518296it [00:17, 1689769.89it/s]
28689002it [00:17, 1694733.56it/s]
28858536it [00:17, 1689612.23it/s]
29028081it [00:17, 1691338.93it/s]
29198858it [00:17, 1696207.68it/s]
29369954it [00:17, 1700610.16it/s]
29540135it [00:17, 1700852.20it/s]
29710563it [00:17, 1701856.69it/s]
29881007it [00:18, 1702619.35it/s]
30051372it [00:18, 1702914.24it/s]
30222867it [00:18, 1706511.72it/s]
30395189it [00:18, 1711512.16it/s]
30566343it [00:18, 1705766.00it/s]
30736926it [00:18, 1705745.48it/s]
30907794it [00:18, 1706610.14it/s]
31078459it [00:18, 1693920.41it/s]
31092874it [00:18, 1657708.29it/s]
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai




[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


tabix -s 1 -b 2 -e 2 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz


seqtool depth_hist     -nbins 500     1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz     > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv


cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md         -output 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.png


[W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi


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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.altera_v3_targets_postQC_hg38.bed.tsv 
seqtool depth_stats  -bed altera_v3_targets_postQC_hg38.bed  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv 
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
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  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv 
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
seqtool read_qc    -bed foresight_clarity_targets_hg38.bed     -n_threads 1     -bam_threads 2     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/read_qc.foresight_clarity_targets_hg38.bed.tsv
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
seqtool reads_per_target     -bed foresight_clarity_targets_hg38.bed     -threads 1     -bam_threads 2     1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/reads_per_target.foresight_clarity_targets_hg38.bed.tsv 
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
seqtool depth_stats  -bed foresight_clarity_targets_hg38.bed  1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/depth_stats.foresight_clarity_targets_hg38.bed.tsv 
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


seqtool gc_bias  -reference Homo_sapiens_assembly38.fasta  -bed foresight_clarity_targets_hg38.bed  -bin_size 0.05  -threads 1  -bam_threads 2  1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv 
[W::hts_idx_load3] The index file is older than the data file: 1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
















cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.FINAL_hotspot_list_07302025_hg38_sorted.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.FINAL_hotspot_list_07302025_hg38_sorted.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 








cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_coding_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_coding_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 




cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_noncoding_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_noncoding_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.altera_v3_targets_postQC_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 




cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.foresight_clarity_targets_hg38.bed.tsv  | plot -x 0  -header infer  -ylim 0 2  -title "1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.foresight_clarity_targets_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 










cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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 "1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed" -output "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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" 






cat 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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 "1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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 "1136_4GR-T1-TDNA-1_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 "1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_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" 


















echo `date` > 1136_4GR-T1-TDNA-1_A23MHWWLT4_1/1136_4GR-T1-TDNA-1_A23MHWWLT4_1.md/qc_complete.txt