.command.log - Workdir - DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1136_7GC-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/d7ecc6af2516d4571433509169e556/.command.log
Size: 33.6 KB
Task: DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1136_7GC-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-rnd-pltf-dev-nextflow-scratch-01/work/ff/87f5f2c5f87d806b00a0a853358d4c/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/55/d7ecc6af2516d4571433509169e556/.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-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-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/55/d7ecc6af2516d4571433509169e556/.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
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/87f5f2c5f87d806b00a0a853358d4c/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
==> STAGING COMPLETE (18 inputs)

mkdir -p 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed


seqtool depth -bam 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam -bed 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz
saturation_plot       -bams 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam       -region chr20       -output 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/saturation_plot.png       -threads 1 
seqtool saturation_metric       -at 1000000       -region chr20       -bam_threads 1       1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/saturation_qc.tsv 
fragment_size       -bams 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam       -region chr20       -output_prefix 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.mpileup && contamination -input 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/contamination.tsv 
seqtool noise   -bam 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam   -ref Homo_sapiens_assembly38.fasta   -region chr20   -include_bed 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/full_bed.bed   -exclude_bed dbsnp138_hg38_common.bed   -threads 1 > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.noise_summary.tsv 
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai

0it [00:00, ?it/s]
148722it [00:00, 1486845.66it/s]
314009it [00:00, 1584473.36it/s]
480754it [00:00, 1622173.32it/s]
651396it [00:00, 1655414.40it/s]
819708it [00:00, 1665346.36it/s]
990210it [00:00, 1678701.64it/s]
1158144it [00:00, 1678895.14it/s]
1326605it [00:00, 1680702.09it/s]
1497924it [00:00, 1690846.89it/s]
1668938it [00:01, 1696790.82it/s]
1838618it [00:01, 1672274.42it/s]
2007505it [00:01, 1677121.84it/s]
2175277it [00:01, 1668318.87it/s]
2342155it [00:01, 1627777.07it/s]
2505150it [00:01, 1620678.71it/s]
2667361it [00:01, 1593527.38it/s]
2833241it [00:01, 1612636.78it/s]
2994663it [00:01, 1565162.70it/s]
3151523it [00:01, 1545502.47it/s]
3313308it [00:02, 1566400.10it/s]
3483553it [00:02, 1606274.36it/s]
3653155it [00:02, 1632754.42it/s]
3825381it [00:02, 1659280.29it/s]
3991499it [00:02, 1652928.44it/s]
4158816it [00:02, 1658902.85it/s]
4324805it [00:02, 1654737.60it/s]
4490348it [00:02, 1555670.62it/s]
4647586it [00:02, 1560438.10it/s]
4806759it [00:02, 1569500.42it/s]
4964355it [00:03, 1543010.98it/s]
5119158it [00:03, 1539741.07it/s]
5278375it [00:03, 1555100.60it/s]
5444150it [00:03, 1585153.42it/s]
5606245it [00:03, 1595758.17it/s]
5773934it [00:03, 1619893.08it/s]
5936070it [00:03, 1569573.46it/s]
6101367it [00:03, 1593927.32it/s]
6268128it [00:03, 1615610.70it/s]
6436370it [00:03, 1635159.20it/s]
6600116it [00:04, 1632993.19it/s]
6763575it [00:04, 1557963.88it/s]
6920169it [00:04, 1554553.52it/s]
7083444it [00:04, 1577306.78it/s]
7242473it [00:04, 1581105.53it/s]
7404541it [00:04, 1592668.18it/s]
7565392it [00:04, 1597326.60it/s]
7729029it [00:04, 1608938.46it/s]
7893477it [00:04, 1619532.80it/s]
8055528it [00:04, 1612650.29it/s]
8216866it [00:05, 1501792.34it/s]
8368588it [00:05, 1451873.08it/s]
8515015it [00:05, 1448947.16it/s]
8666614it [00:05, 1468089.62it/s]
8834830it [00:05, 1530122.79it/s]
9006722it [00:05, 1585392.30it/s]
9179484it [00:05, 1627324.71it/s]
9350234it [00:05, 1651062.30it/s]
9519914it [00:05, 1664653.83it/s]
9690442it [00:06, 1676756.15it/s]
9860720it [00:06, 1684513.54it/s]
10029318it [00:06, 1682509.62it/s]
10200226it [00:06, 1690442.46it/s]
10370783it [00:06, 1694960.60it/s]
10541001it [00:06, 1697107.89it/s]
10711334it [00:06, 1698823.73it/s]done loading BEDs.

10883200it [00:06, 1704753.26it/s]
11055223it [00:06, 1709329.37it/s]
11226170it [00:06, 1695698.01it/s]
11397554it [00:07, 1701093.21it/s]
11569331it [00:07, 1706058.96it/s]
11740148it [00:07, 1706676.30it/s]
11912013it [00:07, 1710245.67it/s]
12083049it [00:07, 1708517.13it/s]
12253909it [00:07, 1704101.26it/s]
12424934it [00:07, 1705895.77it/s]
12595530it [00:07, 1697803.94it/s]
12765322it [00:07, 1693257.87it/s]
12935004it [00:07, 1694306.89it/s]
13104442it [00:08, 1691271.60it/s]
13273745it [00:08, 1691783.10it/s]
13442927it [00:08, 1672543.47it/s]
13610993it [00:08, 1674939.42it/s]
13780919it [00:08, 1682171.07it/s]
13950029it [00:08, 1684822.78it/s]
14118685it [00:08, 1685329.43it/s]
14287325it [00:08, 1685634.67it/s]
14457061it [00:08, 1689132.33it/s]
14627275it [00:08, 1693015.96it/s]
14797644it [00:09, 1696183.24it/s]
14967267it [00:09, 1693511.50it/s]
15136623it [00:09, 1691382.45it/s]
15309634it [00:09, 1702965.09it/s]
15483854it [00:09, 1714705.16it/s]
15655330it [00:09, 1704761.21it/s]
15825822it [00:09, 1696986.01it/s]
15995537it [00:09, 1692794.07it/s]
16164828it [00:09, 1692131.58it/s]
16334097it [00:09, 1692248.20it/s]
16503327it [00:10, 1685398.97it/s]
16671875it [00:10, 1618390.67it/s]
16834261it [00:10, 1615434.27it/s]
17004671it [00:10, 1641376.90it/s]
17173859it [00:10, 1656251.51it/s]
17342542it [00:10, 1665303.90it/s]
17510721it [00:10, 1670196.28it/s]
17677878it [00:10, 1666672.30it/s]
17844641it [00:10, 1662285.88it/s]
18018782it [00:10, 1685867.97it/s]
18192318it [00:11, 1700638.45it/s]
18366948it [00:11, 1714284.31it/s]
18539280it [00:11, 1716975.12it/s]
18711006it [00:11, 1708779.22it/s]
18882377it [00:11, 1710239.02it/s]
19053875it [00:11, 1711541.46it/s]
19225447it [00:11, 1712779.29it/s]
19396736it [00:11, 1692212.00it/s]
19566018it [00:11, 1665118.93it/s]
19732647it [00:11, 1662880.80it/s]
19899014it [00:12, 1652989.79it/s]
20064369it [00:12, 1643668.26it/s]
20234413it [00:12, 1660359.10it/s]
20404804it [00:12, 1673185.19it/s]
20575685it [00:12, 1683785.29it/s]
20744524it [00:12, 1685028.58it/s]
20914623it [00:12, 1689685.40it/s]
21086253it [00:12, 1697638.53it/s]
21256548it [00:12, 1699217.57it/s]
21426483it [00:12, 1672141.29it/s]
21595765it [00:13, 1678162.60it/s]
21765459it [00:13, 1683735.15it/s]
21934391it [00:13, 1685386.67it/s]
22104329it [00:13, 1689553.06it/s]
22273317it [00:13, 1689312.81it/s]
22442271it [00:13, 1688317.36it/s]
22611119it [00:13, 1682517.48it/s]
22779386it [00:13, 1674285.51it/s]
22952152it [00:13, 1690158.31it/s]
23124282it [00:13, 1699329.14it/s]
23296106it [00:14, 1704854.16it/s]
23467428it [00:14, 1707345.45it/s]
23638174it [00:14, 1687518.42it/s]
23807818it [00:14, 1690123.90it/s]
23977713it [00:14, 1692649.12it/s]
24149242it [00:14, 1699392.39it/s]
24319499it [00:14, 1700332.16it/s]
24489551it [00:14, 1688110.72it/s]
24658393it [00:14, 1686565.29it/s]
24829396it [00:15, 1693557.93it/s]
25000148it [00:15, 1697721.64it/s]
25171772it [00:15, 1703105.07it/s]
25343149it [00:15, 1706252.64it/s]
25513783it [00:15, 1698978.54it/s]
25683693it [00:15, 1693961.10it/s]
25853100it [00:15, 1689344.19it/s]
26022043it [00:15, 1668901.63it/s]
26188985it [00:15, 1632573.65it/s]
26359828it [00:15, 1654644.79it/s]
26532885it [00:16, 1676986.77it/s]
26704548it [00:16, 1688725.28it/s]
26874117it [00:16, 1690786.87it/s]
27043286it [00:16, 1607974.50it/s]
27204961it [00:16, 1565940.04it/s][W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai

27377262it [00:16, 1610846.34it/s]
27548883it [00:16, 1641394.17it/s]
27716854it [00:16, 1652607.71it/s]
27886194it [00:16, 1664633.70it/s]
28055755it [00:16, 1673792.66it/s]
28225664it [00:17, 1681309.36it/s]
28397484it [00:17, 1692294.03it/s]
28567883it [00:17, 1695778.23it/s]
28737620it [00:17, 1696052.87it/s]
28907292it [00:17, 1684543.09it/s]
29081177it [00:17, 1700721.07it/s]
29253924it [00:17, 1708699.85it/s]
29424836it [00:17, 1708330.22it/s]
29595698it [00:17, 1685972.35it/s]
29766250it [00:17, 1691762.51it/s]
29935490it [00:18, 1644886.77it/s]
30103246it [00:18, 1654433.18it/s]
30274079it [00:18, 1670308.80it/s]
30445390it [00:18, 1682978.70it/s]
30616086it [00:18, 1690022.26it/s]
30785200it [00:18, 1688058.05it/s]
30957162it [00:18, 1697464.02it/s]
31127993it [00:18, 1700696.59it/s]
31298106it [00:18, 1700158.45it/s]
31469353it [00:18, 1703740.10it/s]
31639855it [00:19, 1704114.24it/s]
31812133it [00:19, 1709696.31it/s]
31983896it [00:19, 1711990.70it/s]
32155104it [00:19, 1707448.11it/s]
32326106it [00:19, 1708207.45it/s]
32487436it [00:19, 1660498.16it/s]


[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


tabix -s 1 -b 2 -e 2 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz


seqtool depth_hist     -nbins 500     1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz     > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv


cat 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth_hist.tsv | plot         -x 0         -xlabel Depth -ylabel "Number of Sites"         -xlim 0 2000         -title 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md         -output 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
seqtool read_qc    -bed foresight_clarity_targets_hg38.bed     -n_threads 1     -bam_threads 2     1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
seqtool reads_per_target     -bed foresight_clarity_targets_hg38.bed     -threads 1     -bam_threads 2     1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
seqtool depth_stats  -bed foresight_clarity_targets_hg38.bed  1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.depth.gz> 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam  > 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai


















cat 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "FINAL_hotspot_list_07302025_hg38_sorted.bed" -output "1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_noncoding_postQC_hg38.bed" -output "1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "foresight_clarity_targets_hg38.bed" -output "1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.foresight_clarity_targets_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






cat 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_coding_postQC_hg38.bed" -output "1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "altera_v3_targets_postQC_hg38.bed" -output "1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias.altera_v3_targets_postQC_hg38.bed.png"  -ylabel "Fold enrichment / depletion"  -xlabel "GC Quantile" 






cat 1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1.md" -suptitle "xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed" -output "1136_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-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_7GC-T1-TDNA-1_A23MHWWLT4_1/1136_7GC-T1-TDNA-1_A23MHWWLT4_1.md/qc_complete.txt