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Merge pull request #466 from genomic-medicine-sweden/develop
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chore: dev to master
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@jonca79
jonca79 authored Jun 10, 2024
2 parents 7634269 + c6d8fa7 commit 2c66e80
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2 changes: 2 additions & 0 deletions .tests/integration/DATA/cnv_deletion_genes2.tsv
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#gene(s) chrmosome start_cnv_region stop_cnv_region gene_start gene_end
TP53 chr17 4638383 10578134 7572906 7579932
3 changes: 3 additions & 0 deletions .tests/integration/DATA/small_deletions_caller_blacklist.tsv
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gene chromosome start_pos end_pos
BAP1 chr3 52436283 52443914
TP53 chr17 7572906 7579932
7 changes: 3 additions & 4 deletions .tests/integration/config/config.yaml
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Expand Up @@ -109,11 +109,10 @@ hotspot_annotation:
hotspots: "DATA/Hotspots_combined.csv"
chr_translation_file: "../../config/reports/hotspot_report.chr.translation.hg19"

hotspot_info:
hotspot_mutations: "DATA/Hotspots_combined.csv"

hotspot_report:
hotspot_mutations: "DATA/Hotspots_combined.csv"
hotspot_mutations:
all: "DATA/Hotspots_combined.csv"
ENC: "DATA/Hotspots_combined.csv"
report_config: "../../config/reports/config/reports/hotspot_report.yaml"
chr_translation_file: "../../reports/config/reports/hotspot_report.chr.translation.hg19"
levels:
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8 changes: 8 additions & 0 deletions .tests/jenkins/Jenkinsfile
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Expand Up @@ -18,6 +18,14 @@ pipeline {
virtualenv venv -p python3.9
source venv/bin/activate
pip3 install -r requirements.txt
hydra-genetics --debug references download -o /beegfs-storage/design_and_ref_files -v config/references/design_files.hg19.yaml
hydra-genetics --debug references download -o /beegfs-storage/design_and_ref_files -v config/references/nextseq.hg19.pon.yaml
hydra-genetics --debug references download -o /beegfs-storage/design_and_ref_files -v config/references/novaseq.hg19.pon.yaml
hydra-genetics --debug references download -o /beegfs-storage/design_and_ref_files -v config/references/design_files.hg38.yaml
hydra-genetics --debug references download -o /beegfs-storage/design_and_ref_files -v config/references/nextseq.hg38.pon.yaml
#hydra-genetics --debug references download -o /beegfs-storage/design_and_ref_files -v config/references/novaseq.hg38.pon.yaml
mkdir -p develop/slurm_out
cp -r config develop/
cp .tests/jenkins/units_develop.tsv develop/units.tsv
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26 changes: 14 additions & 12 deletions .tests/jenkins/test_input_develop.tsv
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Expand Up @@ -4,16 +4,17 @@ bam_rna/SeraSeq-NTRK-FFPE-2-5M_R.star_fusion.bam 7be7432fe3d040f81bbd240452f7463
results/dna/VAL2022-2-5M_T/additional_files/biomarker/VAL2022-2-5M_T.pathology.scarhrd_cnvkit_score.txt 748d10cd1ae3ab6cb7849cfd0e9f39c0
results/dna/VAL2022-2-5M_T/additional_files/biomarker/VAL2022-2-5M_T.purecn.scarhrd_cnvkit_score.txt 55145eab2e60e588c66b233cf1479287
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.amplifications.tsv f397f92f69100d1f20ca65ffac830dd0
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.deletions.tsv f887194ae8134c8a1c8fd427ae533646
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.manta_tumorSV.vcf.gz 1c4f0a2b346d1355dc76fcd126222729
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 2b09144044b2bdf63c440082be760b26
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv ceb3be1abd7951617928cd5c3572a8a1
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv 8a85c32ff5b4e0668376043e16dc0e77
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.svdb_query.vcf c5ebcc72790e0c6f5186298bf5890348
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.svdb_query.vcf c51a58f9332c9176b0f354a955fd25bc
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv 8a85c32ff5b4e0668376043e16dc0e77
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 2438c93ab15eb0e2f6595ac5c006a1f2
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.svdb_query.vcf 49498b22ca7af9176b31e194ef5eb42f
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.deletions.tsv e441b862e6d6d573d18fe40f1eaa7103
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.manta_tumorSV.vcf.gz 05c5aead798d0a04dc762657fc377f70
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_all.cnv_report.tsv 29beb70a92981779b52d26f5b3a38434
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.amp_all_del_validated.cnv_report.tsv 1bb1a34245f59a884358fb21ff2a5f69
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_all.cnv_report.tsv 1115cf9989f5ce9725bf69f2e397fde9
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology_purecn.svdb_query.vcf 9a4d542bbb31bb6adf8178ffe6cf323a
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.pathology.svdb_query.vcf dd3c24e0c05d79eb7a2d9ca02aa73156
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_all.cnv_report.tsv 1115cf9989f5ce9725bf69f2e397fde9
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.amp_all_del_validated.cnv_report.tsv 227717b4bc1de967c6ebeff9e240a274
results/dna/VAL2022-2-5M_T/additional_files/cnv/VAL2022-2-5M_T.purecn.svdb_query.vcf bade0d7c0199cd3d31f0ec2bd4d1b378
results/dna/VAL2022-2-5M_T/additional_files/fusion/VAL2022-2-5M_T.fuseq_wes.unfiltered.results.csv 8ecac127fc74039d5b9eb36e522ac4a5
results/dna/VAL2022-2-5M_T/additional_files/qc/VAL2022-2-5M_T.alignment_summary_metrics.txt fa88f8adc1d6146cf399c6d17a37d098
results/dna/VAL2022-2-5M_T/additional_files/qc/VAL2022-2-5M_T.contamination.table a4ee6cd2e1cfe029229f5b218ac318e9
results/dna/VAL2022-2-5M_T/additional_files/qc/VAL2022-2-5M_T.duplication_metrics.txt 1c476addf89d82bf68aea08eba98aacf
Expand All @@ -28,9 +29,10 @@ results/dna/VAL2022-2-5M_T/additional_files/vcf/vardict_VAL2022-2-5M_T.vcf.gz 22
results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.msisensor_pro.score.tsv e47f1fb00f0220a20335f972e1af8d39
results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.pathology_purecn.scarhrd_cnvkit_score.txt 55145eab2e60e588c66b233cf1479287
results/dna/VAL2022-2-5M_T/biomarker/VAL2022-2-5M_T.TMB.txt e20d98b80deb3ad74605c0439abda1f2
results/dna/VAL2022-2-5M_T/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 2438c93ab15eb0e2f6595ac5c006a1f2
results/dna/VAL2022-2-5M_T/cnv/VAL2022-2-5M_T.pathology_purecn.amp_all_del_validated.cnv_report.tsv 227717b4bc1de967c6ebeff9e240a274
results/dna/VAL2022-2-5M_T/fusion/VAL2022-2-5M_T.fuseq_wes.report.csv ada3432e93dd1ff64f9254d8c83c91c5
results/dna/VAL2022-2-5M_T/qc/VAL2022-2-5M_T.coverage_and_mutations.tsv 62666e179f8e43450e4dd65a75928e34
results/dna/VAL2022-2-5M_T/qc/VAL2022-2-5M_T.coverage_and_mutations.tsv 8921f53aa4902a009fb34b6e6db2a8da
results/dna/VAL2022-2-5M_T/qc/VAL2022-2-5M_T.coverage_and_mutations.ENC.tsv 5331bcd5647fac6ee1424b07b3a81651
results/dna/VAL2022-2-5M_T/vcf/VAL2022-2-5M_T.annotated.exon_only.filter.hard_filter.codon_snv.qci.vcf e9dc0afeeb5d2b738183ce465973b292
results/dna/VAL2022-2-5M_T/vcf/VAL2022-2-5M_T.annotated.exon_only.filter.hard_filter.codon_snv.vcf 7c62b3abce55f9eacce567211dbb0a1b
results/rna/SeraSeq-NTRK-FFPE-2-5M_R/additional_files/fusion/SeraSeq-NTRK-FFPE-2-5M_R.arriba.fusions.tsv eedffe64014818557f8fd9ea2c21fa7c
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4 changes: 4 additions & 0 deletions .tests/jenkins/test_input_main.tsv
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Expand Up @@ -17,6 +17,7 @@ results/dna/HD827_T/additional_files/cnv/HD827_T.pathology.svdb_query.vcf 2c73b0
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.amp_all_del_all.cnv_report.tsv 01660be1832c394b02e87e47e11afd9a
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.amp_all_del_validated.cnv_report.tsv 83f8461e2ac1537ed67f5fbb48cc6e09
results/dna/HD827_T/additional_files/cnv/HD827_T.purecn.svdb_query.vcf 9e1269f0072aa92eeaf969432af18ad8
results/dna/HD827_T/additional_files/fusion/HD827_T.fuseq_wes.unfiltered.results.csv 3350bfff935006e7375301954261e468
results/dna/HD827_T/additional_files/qc/HD827_T.alignment_summary_metrics.txt 351f113346779003eae764ab6d16c5c4
results/dna/HD827_T/additional_files/qc/HD827_T.contamination.table 3c9511e7efab4fefd32144ff2ad19d19
results/dna/HD827_T/additional_files/qc/HD827_T.duplication_metrics.txt 9ac673f2e7d28e6d9601bc096b7764e4
Expand Down Expand Up @@ -49,6 +50,7 @@ results/dna/HD832_T/additional_files/cnv/HD832_T.pathology.svdb_query.vcf ed9da0
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.amp_all_del_all.cnv_report.tsv eb1ad324eff1937f3e6db0c6cbb83aba
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.amp_all_del_validated.cnv_report.tsv 4ba0962054a276e1cfdb4298ef815240
results/dna/HD832_T/additional_files/cnv/HD832_T.purecn.svdb_query.vcf c9e96e55f8d252282ee43004710d731f
results/dna/HD832_T/additional_files/fusion/HD832_T.fuseq_wes.unfiltered.results.csv 23ac6dddb35fb8067fa79465fb6f6acf
results/dna/HD832_T/additional_files/qc/HD832_T.alignment_summary_metrics.txt 8b2548b05cc43eaff20aeabb16aa1490
results/dna/HD832_T/additional_files/qc/HD832_T.contamination.table 18bef22a4210099ec22b2444e6ac2482
results/dna/HD832_T/additional_files/qc/HD832_T.duplication_metrics.txt 20cd0962dab4ca0011aec2100f4a572e
Expand Down Expand Up @@ -81,6 +83,7 @@ results/dna/NA12878_T/additional_files/cnv/NA12878_T.pathology.svdb_query.vcf 7d
results/dna/NA12878_T/additional_files/cnv/NA12878_T.purecn.amp_all_del_all.cnv_report.tsv c626b45394631f05c401350305511bf0
results/dna/NA12878_T/additional_files/cnv/NA12878_T.purecn.amp_all_del_validated.cnv_report.tsv 76bdd87a4ed97e304a79e6ff2b3279d5
results/dna/NA12878_T/additional_files/cnv/NA12878_T.purecn.svdb_query.vcf 8b6a8f92b09c532570e93a1d6f0e6b73
results/dna/NA12878_T/additional_files/fusion/NA12878_T.fuseq_wes.unfiltered.results.csv 003e8f796c80c7e52322630800d36d41
results/dna/NA12878_T/additional_files/qc/NA12878_T.alignment_summary_metrics.txt 3256b89a54ac29cf4f7ef0d6551a3be3
results/dna/NA12878_T/additional_files/qc/NA12878_T.contamination.table e2ab7189dcf7c8cfb1f0ac24ac8766dc
results/dna/NA12878_T/additional_files/qc/NA12878_T.duplication_metrics.txt 355ba5b555b9d83a5820f054c323eef6
Expand Down Expand Up @@ -113,6 +116,7 @@ results/dna/VAL2022_T/additional_files/cnv/VAL2022_T.pathology.svdb_query.vcf eb
results/dna/VAL2022_T/additional_files/cnv/VAL2022_T.purecn.amp_all_del_all.cnv_report.tsv 21a1a191bbd182e974888af7fd35842b
results/dna/VAL2022_T/additional_files/cnv/VAL2022_T.purecn.amp_all_del_validated.cnv_report.tsv badb0ef5f90cf55dc80fafeb9c415787
results/dna/VAL2022_T/additional_files/cnv/VAL2022_T.purecn.svdb_query.vcf abde954047d0b215e596d6305a96ed62
results/dna/VAL2022_T/additional_files/fusion/VAL2022_T.fuseq_wes.unfiltered.results.csv a29ae481538efadb7403814d9d8f76e9
results/dna/VAL2022_T/additional_files/qc/VAL2022_T.alignment_summary_metrics.txt 6c99476824c691ca10e75382ed9bb059
results/dna/VAL2022_T/additional_files/qc/VAL2022_T.contamination.table c1d8fc1cdb993dda50a430028277c37b
results/dna/VAL2022_T/additional_files/qc/VAL2022_T.duplication_metrics.txt 31611542aafb4495560e062cac828f08
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136 changes: 136 additions & 0 deletions .tests/units/gatk_cnv/HD832.HES45_T.filter10.tsv
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@HD VN:1.6
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@SQ SN:chrM LN:16571
@RG ID:GATKCopyNumber SM:VAL-69_T
CONTIG START END LOG2_COPY_RATIO
chr17 7132712 7133612 0.105974
chr17 7215805 7216253 -0.076869
chr17 7216254 7216487 -0.053930
chr17 7216488 7216654 0.085837
chr17 7216655 7216837 -0.027169
chr17 7216838 7217132 0.060059
chr17 7217133 7217353 0.041558
chr17 7217354 7217544 0.016901
chr17 7217545 7217764 -0.005309
chr17 7217765 7218097 0.070831
chr17 7218098 7218641 -0.005943
chr17 7387814 7388446 0.207122
chr17 7398990 7399460 -0.162797
chr17 7399461 7399712 -0.146018
chr17 7399713 7400007 0.145977
chr17 7400008 7400519 0.184896
chr17 7400520 7400902 0.232086
chr17 7400903 7401293 0.073453
chr17 7401294 7401799 -0.038963
chr17 7402088 7402541 0.008168
chr17 7402542 7403080 0.062317
chr17 7403688 7404213 0.036523
chr17 7404214 7404517 0.116535
chr17 7404518 7404773 0.183643
chr17 7404774 7405133 0.198395
chr17 7405134 7405639 0.174971
chr17 7405640 7406230 0.086756
chr17 7406231 7406657 0.090217
chr17 7406658 7406857 0.008901
chr17 7406858 7407380 0.081301
chr17 7411300 7412028 0.239698
chr17 7412029 7412680 0.074670
chr17 7412681 7413221 -0.044962
chr17 7414264 7414681 0.093942
chr17 7414682 7415018 0.157573
chr17 7415019 7415405 0.059885
chr17 7415406 7415729 0.099066
chr17 7415730 7416001 0.160210
chr17 7416002 7416291 0.185480
chr17 7416292 7417766 -0.202713
chr17 7460067 7460967 0.091835
chr17 7572657 7573278 -0.019844
chr17 7573657 7574303 0.151558
chr17 7576267 7576604 -0.217493
chr17 7576756 7576972 -0.000587
chr17 7576973 7577327 -0.091586
chr17 7577328 7577878 -0.098413
chr17 7577907 7578330 -0.089749
chr17 7578331 7578824 -0.158608
chr17 7579042 7579645 -0.408962
chr17 7579646 7579780 -0.977634
chr17 7579781 7580182 0.222077
chr17 7787855 7788671 -0.883565
chr17 7792049 7792688 0.397481
chr17 7792712 7793364 0.253649
chr17 7793619 7794158 -0.463637
chr17 7794159 7794652 0.207440
chr17 7796334 7797005 -0.169586
chr17 7797006 7797343 0.155267
chr17 7797344 7797658 0.064223
chr17 7797659 7798080 -0.020076
chr17 7798081 7798562 0.111615
chr17 7798563 7799130 -0.329941
chr17 7800131 7800882 0.151060
chr17 7801019 7801617 0.083185
chr17 7801618 7802121 0.043944
chr17 7802122 7802590 -0.051191
chr17 7802591 7803037 0.184511
chr17 7803038 7803479 0.213696
chr17 7803480 7803802 0.026167
chr17 7803803 7804109 0.232087
chr17 7804110 7804436 0.007232
chr17 7804437 7804963 0.035956
chr17 7805658 7806150 0.023346
chr17 7806151 7806484 0.056706
chr17 7806485 7806982 0.078185
chr17 7806983 7807534 0.124214
chr17 7807535 7808177 0.156872
chr17 7808178 7808711 0.105312
chr17 7808712 7809099 0.169250
chr17 7809100 7809577 0.287494
chr17 7809601 7810101 0.139272
chr17 7810102 7810396 0.177454
chr17 7810397 7810618 0.350710
chr17 7810619 7810862 0.144804
chr17 7810863 7811116 0.105927
chr17 7811117 7811528 0.216446
chr17 7811529 7811921 0.289250
chr17 7811922 7812304 0.269335
chr17 7812305 7812926 0.077875
chr17 7813476 7814037 0.272691
chr17 7814038 7814536 0.167095
chr17 7814537 7815173 0.103120
chr17 7975819 7976367 0.149621
chr17 7976368 7976805 -0.099943
chr17 7976806 7977345 0.085893
chr17 7978643 7979263 -0.053568
chr17 7979264 7979818 0.070835
chr17 7979819 7980184 -0.034290
chr17 7980185 7980781 0.119204
chr17 7982444 7982972 0.092477
chr17 7982973 7983406 0.366159
chr17 7983407 7983816 0.249227
chr17 7983817 7984150 -0.023842
chr17 7984151 7984359 -0.269555
chr17 7984360 7984775 -0.041958
chr17 7989064 7989808 0.103631
chr17 7990344 7991030 -0.396831
16 changes: 11 additions & 5 deletions config/config.data.hg19.yaml
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Expand Up @@ -54,13 +54,14 @@ bwa_mem:
sa: "{{PROJECT_REF_DATA}}/ref_data/hg19/hg19.with.mt.fasta.sa"

call_small_cnv_deletions:
blacklist: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/small_deletions_caller_blacklist.tsv"
regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_deletion_genes.tsv"

call_small_cnv_amplifications:
regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_240307.tsv"

cnvkit_batch:
normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_36.cnn"
normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_PoN_combined_hg19.cnn"

cnvkit_batch_hrd:
normal_reference_hrd: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_27_HRD.cnn"
Expand All @@ -77,6 +78,12 @@ filter_fuseq_wes:
transcript_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_transcript_black_list.txt"
gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg19.refGene.gtf"

filter_fuseq_wes_umi:
gene_fusion_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/false_positive_fusion_pairs.txt"
gene_white_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_gene_white_list.txt"
transcript_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_transcript_black_list.txt"
gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg19.refGene.gtf"

fuseq_wes:
ref_json: "{{PROJECT_REF_DATA}}/ref_data/fuseq_wes/UCSC_hg19_wes_contigSize3000_bigLen130000_r100.json"
gtfSqlite: "{{PROJECT_REF_DATA}}/ref_data/fuseq_wes/UCSC_hg19_wes_contigSize3000_bigLen130000_r100.sqlite"
Expand Down Expand Up @@ -105,12 +112,11 @@ hotspot_annotation:
chr_translation_file: "config/reports/hotspot_report.chr.translation.hg19"
hotspots: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011.csv"

hotspot_info:
hotspot_mutations: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011.csv"

hotspot_report:
chr_translation_file: "config/reports/hotspot_report.chr.translation.hg19"
hotspot_mutations: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011.csv"
hotspot_mutations:
all: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011.csv"
ENC: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/ENC_hotspots_240604.csv"

manta_config_t:
extra: "--exome --callRegions {{PROJECT_DESIGN_DATA}}/GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.210608.bed.gz"
Expand Down
20 changes: 15 additions & 5 deletions config/config.data.hg38.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -54,13 +54,14 @@ bwa_mem:
sa: "{{PROJECT_REF_DATA}}/ref_data/GRCh38_p14/homo_sapiens.fasta.sa"

call_small_cnv_deletions:
blacklist: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/small_deletions_caller_blacklist_hg38.tsv"
regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_deletion_genes_hg38.tsv"

call_small_cnv_amplifications:
regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_hg38_240307.tsv"

cnvkit_batch:
normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn"
normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_PoN_combined_hg38.cnn"

cnvkit_batch_hrd:
normal_reference_hrd: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_nextseq_noUmea_27_hg38.cnn"
Expand All @@ -77,6 +78,12 @@ filter_fuseq_wes:
transcript_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_transcript_black_list.txt"
gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg38.refGene.gtf"

filter_fuseq_wes_umi:
gene_fusion_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/false_positive_fusion_pairs.txt"
gene_white_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_gene_white_list.txt"
transcript_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_transcript_black_list.txt"
gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg38.refGene.gtf"

fuseq_wes:
ref_json: "{{PROJECT_REF_DATA}}/ref_data/fuseq_wes/UCSC_hg38_wes_contigSize3000_bigLen130000_r100.json"
gtfSqlite: "{{PROJECT_REF_DATA}}/ref_data/fuseq_wes/UCSC_hg38_wes_contigSize3000_bigLen130000_r100.sqlite"
Expand All @@ -97,16 +104,19 @@ gatk_get_pileup_summaries:
sites: "{{PROJECT_REF_DATA}}/ref_data/GNOMAD/small_exac_common_3.hg38.vcf.gz"
variants: "{{PROJECT_REF_DATA}}/ref_data/GNOMAD/small_exac_common_3.hg38.vcf.gz"

gene_fuse:
genes: "/projects/wp1/nobackup/ngs/utveckling/Twist_DNA_DATA/gene_fuse/GMS560_fusion_w_pool2.hg38.csv"
fasta: "/data/ref_genomes/GRCh38_p14/homo_sapiens.fasta"

hotspot_annotation:
chr_translation_file: "config/reports/hotspot_report.chr.translation.hg38"
hotspots: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv"

hotspot_info:
hotspot_mutations: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv"

hotspot_report:
chr_translation_file: "config/reports/hotspot_report.chr.translation.hg38"
hotspot_mutations: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv"
hotspot_mutations:
all: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv"
ENC: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/ENC_hotspots_240604_hg38.csv"

manta_config_t:
extra: "--exome --callRegions {{PROJECT_DESIGN_DATA}}/GMS560/design/pool1_pool2.sort.merged.padded20.cnv200.hg38.split_fusion_genes.reannotated.230222.bed.gz"
Expand Down
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