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AN-415 Eliminate reliance on test data from gs://broad-public-datasets (#7696)
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-104
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4 files changed

+105
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‎centaur/src/main/resources/standardTestCases/reference_disk/gcpbatch_reference_disk_mounted_only_if_requested.wdl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ task MentionsNirvanaReference {
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input {
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# Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
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File mention =
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"gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
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"gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
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}
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command <<<
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PS4='\D{+%F %T} \w $ '

‎centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ task MentionsNirvanaReference {
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input {
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# Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
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File mention =
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"gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
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"gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
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}
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command <<<
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PS4='\D{+%F %T} \w $ '

‎centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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{
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"wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
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"wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
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"wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
3+
"wf_reference_disk_test.nirvana_reference_file_input": "gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
4+
"wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
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}

‎src/ci/resources/google_reference_image_manifest.conf‎

Lines changed: 101 additions & 100 deletions
Original file line numberDiff line numberDiff line change
@@ -191,156 +191,157 @@ reference-disk-localization-manifests = [
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}
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]
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},
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# Copied from Prod config `_cromwell-reference-images.conf.tpl` (WX-1505)
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{
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"imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-02-01",
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"diskSizeGb" : 55,
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"imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2024-03-06-public-2024-03-12",
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diskSizeGb: 55
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"files" : [ {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd",
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"crc32c" : 1502286599
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/Cache/GRCh38/Both.polyphen.ndb"
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crc32c: 3178180885
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
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"crc32c" : 2106006282
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/Cache/GRCh38/Both.sift.ndb"
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crc32c: 2786880382
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_gene_scores_2.1.nga",
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"crc32c" : 3393536227
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/Cache/GRCh38/Both.transcripts.ndb"
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crc32c: 2114520493
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa",
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"crc32c" : 2371255414
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/References/Homo_sapiens.GRCh38.Nirvana.dat"
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crc32c: 1694422311
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma.idx",
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"crc32c" : 3985843783
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
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crc32c: 2492681982
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/References/Homo_sapiens.GRCh38.Nirvana.dat",
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"crc32c" : 1694422311
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa"
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crc32c: 2371255414
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.sift.ndb",
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"crc32c" : 2786880382
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa.idx"
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crc32c: 870728029
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nsi",
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"crc32c" : 3787486272
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma"
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crc32c: 1696693985
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa",
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"crc32c" : 3105778103
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma.idx"
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crc32c: 3985843783
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa",
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"crc32c" : 1821283507
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/COSMIC_GeneFusions_94.gfj"
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crc32c: 429830169
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa",
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"crc32c" : 1393836085
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_20160414.nsi"
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crc32c: 1181611304
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa",
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"crc32c" : 2730251112
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20231105.nga"
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crc32c: 2121701417
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.transcripts.ndb",
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"crc32c" : 2114520493
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20231105.nsi"
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crc32c: 3746920330
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MultiZ100Way_20171006.pcs",
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"crc32c" : 1251171842
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinGen_disease_validity_curations_20231105.nga"
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crc32c: 1696736207
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa.idx",
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"crc32c" : 2183408606
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinVar_20231028.nsa"
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crc32c: 1077441598
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa",
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"crc32c" : 482110804
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinVar_20231028.nsa.idx"
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crc32c: 1794906589
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa",
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"crc32c" : 1654978963
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/ClinVar_20231028.nsi"
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crc32c: 622362682
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.polyphen.ndb",
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"crc32c" : 3178180885
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa"
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crc32c: 3457097933
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa.idx",
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"crc32c" : 3807477399
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa.idx"
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crc32c: 245207854
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_SV_2.1.nsi",
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"crc32c" : 2600275374
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/DECIPHER_201509.nsi"
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crc32c: 2426309371
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_disease_validity_curations_20220512.nga",
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"crc32c" : 4116422668
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/FusionCatcher_1.33.gfs"
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crc32c: 1420426876
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/OMIM_20220516.nga",
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"crc32c" : 1767833806
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/GME_20160618.nsa"
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crc32c: 1210977352
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa",
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"crc32c" : 710316739
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/GME_20160618.nsa.idx"
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crc32c: 1732177354
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa.idx",
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"crc32c" : 1732177354
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa"
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crc32c: 2730251112
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa.idx",
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"crc32c" : 245207854
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa.idx"
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crc32c: 3139541733
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa",
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"crc32c" : 4136875677
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa"
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crc32c: 1721491427
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsi",
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"crc32c" : 1056818502
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
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crc32c: 2375984948
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa",
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"crc32c" : 1210977352
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MITOMAP_SV_20200819.nsi"
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crc32c: 1378887803
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa.idx",
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"crc32c" : 870728029
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/MultiZ100Way_20171006.pcs"
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crc32c: 1251171842
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_LCR_2.1.lcr",
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"crc32c" : 3602069872
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/OMIM_20220516.nga"
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crc32c: 1767833806
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa.idx",
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"crc32c" : 2835194789
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa"
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crc32c: 4136875677
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nga",
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"crc32c" : 2485206803
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa.idx"
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crc32c: 2835194789
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_SV_20200819.nsi",
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"crc32c" : 1378887803
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa"
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crc32c: 710316739
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa.idx",
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"crc32c" : 302652747
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa.idx"
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crc32c: 302652747
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_20160414.nsi",
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"crc32c" : 1181611304
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa"
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crc32c: 3105778103
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa.idx",
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"crc32c" : 980438557
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa.idx"
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crc32c: 980438557
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DECIPHER_201509.nsi",
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"crc32c" : 2426309371
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa"
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crc32c: 1393836085
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa",
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"crc32c" : 3457097933
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa.idx"
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crc32c: 3807477399
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa.idx",
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"crc32c" : 3582543830
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa"
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crc32c: 1821283507
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/COSMIC_GeneFusions_94.gfj",
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"crc32c" : 429830169
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa.idx"
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crc32c: 37093822
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa.idx",
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"crc32c" : 37093822
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path: "gcp-public-data--broad-references/hg38/v0/Nirvana/3.18.1_2024-03-06/SupplementaryAnnotation/GRCh38/dbSNP_156.nsa"
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crc32c: 579363434
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}, {
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"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/FusionCatcher_1.33.gfs",
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