Skip to content

Commit

Permalink
Genotype concordance workflows (#414)
Browse files Browse the repository at this point in the history
  • Loading branch information
@mwalker174
mwalker174 authored Sep 27, 2022
1 parent 6463818 commit 1f1a3b3
Show file tree
Hide file tree
Showing 8 changed files with 629 additions and 61 deletions.
19 changes: 19 additions & 0 deletions inputs/templates/test/JoinRawCalls/JoinRawCalls.json.tmpl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
{
"JoinRawCalls.gatk_docker":{{ dockers.gatk_docker | tojson }},
"JoinRawCalls.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
"JoinRawCalls.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},

"JoinRawCalls.clustered_depth_vcfs" : [{{ test_batch.merged_depth_vcf | tojson }}],
"JoinRawCalls.clustered_manta_vcfs" : [{{ test_batch.merged_manta_vcf | tojson }}],
"JoinRawCalls.clustered_wham_vcfs" : [{{ test_batch.merged_wham_vcf | tojson }}],
"JoinRawCalls.clustered_melt_vcfs" : [{{ test_batch.merged_melt_vcf | tojson }}],

"JoinRawCalls.ploidy_table": {{ test_batch.ploidy_table | tojson }},

"JoinRawCalls.contig_list": {{ reference_resources.primary_contigs_list | tojson }},
"JoinRawCalls.reference_fasta": {{ reference_resources.reference_fasta | tojson }},
"JoinRawCalls.reference_fasta_fai": {{ reference_resources.reference_index | tojson }},
"JoinRawCalls.reference_dict": {{ reference_resources.reference_dict | tojson }},

"JoinRawCalls.cohort": {{ test_batch.name | tojson }}
}
22 changes: 22 additions & 0 deletions inputs/templates/test/SVConcordance/SVConcordance.json.tmpl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
{
"SVConcordance.gatk_docker":{{ dockers.gatk_docker_concordance | tojson }},
"SVConcordance.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
"SVConcordance.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
"SVConcordance.sv_utils_docker": {{ dockers.sv_utils_docker | tojson }},

"SVConcordance.eval_vcf" : {{ test_batch.clean_vcf | tojson }},
"SVConcordance.truth_vcf" : {{ test_batch.joined_raw_calls_vcf | tojson }},

"SVConcordance.ploidy_table": {{ test_batch.ploidy_table | tojson }},
"SVConcordance.cohort": {{ test_batch.name | tojson }},

"SVConcordance.run_svutils_truth_vcf": "false",
"SVConcordance.run_formatter_truth_vcf": "false",

"SVConcordance.run_svutils_eval_vcf": "true",
"SVConcordance.run_formatter_eval_vcf": "true",
"SVConcordance.formatter_eval_args": "--only-add-cn-fields --replace-ev-format --filter-unsupported-types",

"SVConcordance.contig_list": {{ reference_resources.primary_contigs_list | tojson }},
"SVConcordance.reference_dict": {{ reference_resources.reference_dict | tojson }}
}
19 changes: 10 additions & 9 deletions inputs/values/dockers.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
"condense_counts_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-36-g88b0578",
"gatk_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-36-g88b0578",
"gatk_docker_pesr_override": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-36-g88b0578",
"gatk_docker_concordance": "us.gcr.io/broad-dsde-methods/markw/gatk:mw-sv-concordance-937c81",
"genomes_in_the_cloud_docker": "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.2-1510681135",
"linux_docker": "marketplace.gcr.io/google/ubuntu1804",
"manta_docker": "us.gcr.io/broad-dsde-methods/manta:8645aa",
Expand All @@ -12,12 +13,12 @@
"samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2022-06-10-v0.23-beta-9c6fbf56",
"sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2022-06-10-v0.23-beta-9c6fbf56",
"sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2022-06-10-v0.23-beta-9c6fbf56",
"sv_pipeline_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-21-v0.26.1-beta-c5e6abc8",
"sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-21-v0.26.1-beta-c5e6abc8",
"sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-21-v0.26.1-beta-c5e6abc8",
"sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-21-v0.26.1-beta-c5e6abc8",
"sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-21-v0.26.1-beta-c5e6abc8",
"sv_pipeline_rdtest_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-21-v0.26.1-beta-c5e6abc8",
"sv_pipeline_base_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-concordance-8223c30",
"sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-concordance-8223c30",
"sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-concordance-8223c30",
"sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-concordance-8223c30",
"sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-concordance-8223c30",
"sv_pipeline_rdtest_docker": "us.gcr.io/broad-dsde-methods/markw/sv-pipeline:mw-concordance-8223c30",
"wham_docker": "us.gcr.io/broad-dsde-methods/wham:8645aa",
"igv_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
"duphold_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",
Expand All @@ -28,8 +29,8 @@
"cnmops-virtual-env": "us.gcr.io/broad-dsde-methods/gatk-sv/cnmops-virtual-env:2022-06-10-v0.23-beta-9c6fbf56",
"sv-pipeline-virtual-env": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline-virtual-env:2022-06-10-v0.23-beta-9c6fbf56",
"samtools-cloud-virtual-env": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud-virtual-env:2022-06-10-v0.23-beta-9c6fbf56",
"sv-utils-env": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-utils-env:2022-09-09-v0.25.1-beta-cd5ce7e0",
"sv_utils_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-utils:2022-09-21-v0.26.1-beta-c5e6abc8",
"sv-utils-env": "us.gcr.io/broad-dsde-methods/markw/sv-utils-env:mw-concordance-7251507",
"sv_utils_docker": "us.gcr.io/broad-dsde-methods/markw/sv-utils:mw-concordance-7251507",
"gq_recalibrator_docker": "us.gcr.io/broad-dsde-methods/tbrookin/gatk:0a7e1d86f",
"str": "us.gcr.io/broad-dsde-methods/gatk-sv/str:2022-09-15-v0.25.1-beta-b53e58af"
"str": "us.gcr.io/broad-dsde-methods/markw/str:mw-concordance-7251507"
}
4 changes: 3 additions & 1 deletion inputs/values/ref_panel_1kg.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1120,6 +1120,7 @@
"hgdp_1kgp_ped": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/HGDP_1KGP.ped",
"cohort_depth_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSamples/FilterBatchSamples/b308c32e-d171-4d8d-aeaf-b561c55b06b4/call-ExcludeOutliers/shard-4/cacheCopy/ref_panel_1kg.depth.outliers_removed.vcf.gz",
"cohort_pesr_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-FilterBatch/FilterBatch/184defa3-e61c-4757-9962-f685f6d0d204/call-FilterBatchSamples/FilterBatchSamples/b308c32e-d171-4d8d-aeaf-b561c55b06b4/call-MergePesrVcfs/cacheCopy/ref_panel_1kg.filtered_pesr_merged.vcf.gz",
"concordance_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/SVConcordance/1509e8d1-5d8a-4455-9cd6-152f4f1af313/ref_panel_1kg.concordance.vcf.gz",
"contig_ploidy_model_tar": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/gcnv/ref_panel_1kg_v2-contig-ploidy-model.tar.gz",
"counts": [
"gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/counts/HG00096.counts.tsv.gz",
Expand Down Expand Up @@ -1585,6 +1586,7 @@
"genotype_pesr_pesr_sepcutoff": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypePESRPart1/GenotypePESRPart1/40ec6d76-dd1c-432d-bfab-bc4426d0b1ec/call-TrainRDGenotyping/TrainRDGenotyping/e5540a96-9072-4719-bcfb-afccdfec15c6/call-UpdateCutoff/cacheCopy/ref_panel_1kg.pesr.pesr_sepcutoff.txt",
"genotyped_depth_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypeDepthPart2/GenotypeDepthPart2/0aafd752-e606-4196-86ac-41c1c3ce1eb2/call-ConcatGenotypedVcfs/cacheCopy/ref_panel_1kg.depth.vcf.gz",
"genotyped_pesr_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypePESRPart2/GenotypePESRPart2/ce1f4075-1a3e-44b5-9cfe-bfb701327616/call-ConcatGenotypedVcfs/cacheCopy/ref_panel_1kg.pesr.vcf.gz",
"joined_raw_calls_vcf": "gs://gatk-sv-ref-panel-1kg/outputs/JoinRawCalls/a613865b-f7ec-4edb-8a2e-21508335249e/ref_panel_1kg.join_raw_calls.vcf.gz",
"manta_vcfs": [
"gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-0/GatherSampleEvidence/bed8ee84-625c-4d39-99d4-20f9c0462ce6/call-Manta/Manta/9729df6e-82b5-40af-b2f2-028de89f2a7d/call-RunManta/cacheCopy/HG00096.manta.vcf.gz",
"gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GatherSampleEvidenceBatch/GatherSampleEvidenceBatch/bb5e70f1-7186-4e29-96f8-dcb9ee000642/call-GatherSampleEvidence/shard-1/GatherSampleEvidence/b623755c-af49-4f7c-98d9-f03d95ab9397/call-Manta/Manta/aaed987f-50bd-48f6-a4c1-181512567c1a/call-RunManta/cacheCopy/HG00129.manta.vcf.gz",
Expand Down Expand Up @@ -2239,7 +2241,7 @@
"name": "ref_panel_1kg",
"outlier_cutoff_table": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v1/module03_outlier_cutoff_table.tsv",
"ped_file": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/ped/1kg_ref_panel_v1.ped",

"ploidy_table": "gs://gatk-sv-ref-panel-1kg/outputs/ClusterBatch/mw-concordance/ref_panel_1kg.ploidy.FEMALE_chrY_1.tsv",
"qc_definitions": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/ref_panel_1kg.qc_definitions.tsv",
"qc_file": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/sv_qc.ref_panel_1kg.tsv",
"raw_sr_background_fail_file": "gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypePESRPart2/GenotypePESRPart2/ce1f4075-1a3e-44b5-9cfe-bfb701327616/call-TripleStreamCatFail/cacheCopy/ref_panel_1kg.genotype_SR_part2_background_fail.txt",
Expand Down
Loading

0 comments on commit 1f1a3b3

Please sign in to comment.