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October 24, 2022 20:09
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Workspace Data TSV for GATK-SV Single Sample pipeline v0.26.1-beta
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| workspace:cloud_sdk_docker | cnmops_docker | condense_counts_docker | gatk_docker | gatk_docker_pesr_override | genomes_in_the_cloud_docker | linux_docker | manta_docker | samtools_cloud_docker | sv_base_docker | sv_base_mini_docker | sv_pipeline_base_docker | sv_pipeline_docker | sv_pipeline_hail_docker | sv_pipeline_updates_docker | sv_pipeline_qc_docker | sv_pipeline_rdtest_docker | wham_docker | ref_panel_name | ref_panel_bincov_matrix | ref_panel_contig_ploidy_model_tar | ref_panel_cutoffs | ref_panel_del_bed | ref_panel_dup_bed | ref_panel_gcnv_model_tars_list | ref_panel_genotype_pesr_pesr_sepcutoff | ref_panel_genotype_pesr_depth_sepcutoff | ref_panel_genotype_depth_pesr_sepcutoff | ref_panel_genotype_depth_depth_sepcutoff | ref_panel_ped_file | ref_panel_PE_files_list | ref_panel_PE_metrics | ref_panel_qc_definitions | ref_panel_requester_pays_crams | ref_panel_samples_list | ref_panel_SD_files_list | ref_panel_SR_files_list | ref_panel_SR_metrics | ref_panel_std_manta_vcf_tar | ref_panel_std_wham_vcf_tar | ref_panel_vcf | reference_name | reference_allosome_file | reference_autosome_file | reference_bin_exclude | reference_cnmops_exclude_list | reference_contig_ploidy_priors | reference_copy_number_autosomal_contigs | reference_cytobands | reference_sd_locs_vcf | reference_depth_exclude_list | reference_empty_file | reference_exclude_intervals_for_gcnv_filter_intervals | reference_external_af_ref_bed | reference_external_af_ref_bed_prefix | reference_genome_file | reference_manta_region_bed | reference_mei_bed | reference_melt_std_vcf_header | reference_noncoding_bed | reference_pesr_exclude_list | reference_preprocessed_intervals | reference_primary_contigs_list | reference_primary_contigs_fai | reference_protein_coding_gtf | reference_dict | reference_fasta | reference_index | reference_version | reference_rmsk | reference_segdups | reference_seed_cutoffs | reference_wgd_scoring_mask | reference_wham_include_list_bed_file | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| google/cloud-sdk | us.gcr.io/broad-dsde-methods/gatk-sv/cnmops:2022-06-10-v0.23-beta-9c6fbf56 | us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-36-g88b0578 | us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-36-g88b0578 | us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-36-g88b0578 | us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.2-1510681135 | marketplace.gcr.io/google/ubuntu1804 | us.gcr.io/broad-dsde-methods/manta:8645aa | us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2022-06-10-v0.23-beta-9c6fbf56 | us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2022-06-10-v0.23-beta-9c6fbf56 | us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2022-06-10-v0.23-beta-9c6fbf56 | us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-13-v0.25.1-beta-f6d0c4da | us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-13-v0.25.1-beta-f6d0c4da | us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-13-v0.25.1-beta-f6d0c4da | us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-13-v0.25.1-beta-f6d0c4da | us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-13-v0.25.1-beta-f6d0c4da | us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2022-09-13-v0.25.1-beta-f6d0c4da | us.gcr.io/broad-dsde-methods/wham:8645aa | ref_panel_1kg | gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-EvidenceQC/EvidenceQC/f7f8f407-0a3c-4c3d-982f-7bd181ac965a/call-MakeBincovMatrix/MakeBincovMatrix/0106cefa-5ebf-4131-9073-15413bf93a83/call-ZPaste/cacheCopy/ref_panel_1kg.RD.txt.gz | gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/gcnv/ref_panel_1kg_v2-contig-ploidy-model.tar.gz | 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-FilterBatchSites/FilterBatchSites/13801c7d-9478-40dc-9a4a-2e80cbab1136/call-AdjudicateSV/cacheCopy/ref_panel_1kg.cutoffs | gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-MergeDepth/MergeDepth/b58e04ee-846d-4be6-bba3-6dda2f2c995e/call-MergeSet_del/cacheCopy/ref_panel_1kg.DEL.bed.gz | gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GATKSVPipelinePhase1/GATKSVPipelinePhase1/acce2c71-7458-4205-ae13-624f6efc9956/call-GatherBatchEvidence/GatherBatchEvidence/366e817a-feb2-4d3c-915c-a8bd25529b81/call-MergeDepth/MergeDepth/b58e04ee-846d-4be6-bba3-6dda2f2c995e/call-MergeSet_dup/cacheCopy/ref_panel_1kg.DUP.bed.gz | gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/gcnv_model_tars_list.txt | 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 | 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.depth_sepcutoff.txt | gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypeDepthPart1/GenotypeDepthPart1/be787bb1-25ff-4a54-92a6-2fa6faaee8ec/call-TrainRDGenotyping/TrainRDGenotyping/aa7bc7f2-9779-4242-aa5d-8a8ea4375af9/call-UpdateCutoff/cacheCopy/ref_panel_1kg.depth.pesr_sepcutoff.txt | gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/call-GenotypeBatch/GenotypeBatch/ad17f522-0950-4f0a-9148-a13f689082ed/call-GenotypeDepthPart1/GenotypeDepthPart1/be787bb1-25ff-4a54-92a6-2fa6faaee8ec/call-TrainRDGenotyping/TrainRDGenotyping/aa7bc7f2-9779-4242-aa5d-8a8ea4375af9/call-UpdateCutoff/cacheCopy/ref_panel_1kg.depth.depth_sepcutoff.txt | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/ped/1kg_ref_panel_v1.ped | gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/pe/PE_files_list.txt | 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-TrainPEGenotyping/TrainPEGenotyping/8c1271fd-027d-4669-b516-b41ee77d8997/call-GenotypePEPart1/cacheCopy/ref_panel_1kg.pe_metric_file.txt | gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/single_sample.qc_definitions.tsv | True | gs://gatk-sv-ref-panel-1kg/outputs/GATKSVPipelineBatch/38c65ca4-2a07-4805-86b6-214696075fef/samples_list.txt | gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/sd/SD_files_list.txt | gs://gatk-sv-ref-panel-1kg/outputs/tws_earlyBAF/sr/SR_files_list.txt | 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-TrainSRGenotyping/TrainSRGenotyping/e81a3092-0c6e-4768-afed-27d7018175dc/call-GenotypeSRPart1/cacheCopy/ref_panel_1kg.sr_metric_file.txt | gs://gatk-sv-ref-panel-1kg/outputs/GatherBatchEvidence/b705e9f6-c401-4a9a-a059-1a68d1ca5f98/ref_panel_1kg.manta_std.tar.gz | gs://gatk-sv-ref-panel-1kg/outputs/GatherBatchEvidence/b705e9f6-c401-4a9a-a059-1a68d1ca5f98/ref_panel_1kg.wham_std.tar.gz | gs://gatk-sv-ref-panel-1kg/outputs/MakeCohortVcf/8a209488-c928-449d-92cd-0a5131e92b7c/call-CleanVcf/CleanVcf/277f3f25-bb99-4fe4-a48b-567fd3f344f9/call-ConcatCleanedVcfs/ref_panel_1kg.cleaned.vcf.gz | resources_hg38 | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/allosome.fai | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/autosome.fai | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/bin_exclude.hg38.gatkcov.bed.gz | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/GRCh38_Nmask.bed | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/hg38.contig_ploidy_priors_homo_sapiens.tsv | 2 | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/cytobands_hg38.bed.gz | gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/depth_blacklist.sorted.bed.gz | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/empty.file | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/hg38.wgs.blacklist.wPAR.bed | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/gnomad_AF/gnomad_v2.1_sv.sites.GRCh38.bed.gz | gnomad_v2.1_sv | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.genome | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/primary_contigs_plus_mito.bed.gz | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/mei_hg38.bed.gz | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/melt_standard_vcf_header.txt | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/noncoding.sort.hg38.bed | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/PESR.encode.peri_all.repeats.delly.hg38.blacklist.sorted.bed.gz | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/preprocessed_intervals.interval_list | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/primary_contigs.list | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/contig.fai | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/MANE.GRCh38.v0.95.select_ensembl_genomic.gtf | gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict | gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta | gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai | 38 | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.randomForest_blacklist.withRepMask.bed.gz | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.SD_gaps_Cen_Tel_Heter_Satellite_lumpy.blacklist.sorted.merged.bed.gz | gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/seed_cutoff.txt | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wgd_scoring_mask.hg38.gnomad_v3.bed | gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wham_whitelist.bed |
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