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GATKSVPipelineSingleSample.wdl.ref_panel_v1b.NA19240.json
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GATKSVPipelineSingleSample.wdl.ref_panel_v1b.NA19240.json
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{
"GATKSVPipelineSingleSample.sample_id" : "SM-GN4BI",
"GATKSVPipelineSingleSample.batch" : "gatk_sv_clinical_v1b",
"GATKSVPipelineSingleSample.bam_or_cram_file" : "gs://fc-dce6617d-8c29-47c3-8da9-ed441f0b7287/Set_4_7_HapMap_samples_3-22-2018/RP-1536/WGS/SM-GN4BI/v1/NA19240_NA19240_1a_SM-GN4BI_v1.cram",
"GATKSVPipelineSingleSample.bam_or_cram_index" : "gs://fc-dce6617d-8c29-47c3-8da9-ed441f0b7287/Set_4_7_HapMap_samples_3-22-2018/RP-1536/WGS/SM-GN4BI/v1/NA19240_NA19240_1a_SM-GN4BI_v1.cram.crai",
"GATKSVPipelineSingleSample.cutoffs" : "gs://gatk-sv-resources/clinical/reference_panel_v2/cutoffs/ref_panel_v2.cutoffs",
"GATKSVPipelineSingleSample.genotype_pesr_pesr_sepcutoff" : "gs://gatk-sv-resources/clinical/reference_panel_v2/cutoffs/genotype_pesr.pesr_sepcutoff.txt",
"GATKSVPipelineSingleSample.genotype_pesr_depth_sepcutoff" : "gs://gatk-sv-resources/clinical/reference_panel_v2/cutoffs/genotype_pesr.depth_sepcutoff.txt",
"GATKSVPipelineSingleSample.genotype_depth_pesr_sepcutoff" : "gs://gatk-sv-resources/clinical/reference_panel_v2/cutoffs/genotype_depth.pesr_sepcutoff.txt",
"GATKSVPipelineSingleSample.genotype_depth_depth_sepcutoff" : "gs://gatk-sv-resources/clinical/reference_panel_v2/cutoffs/genotype_depth.depth_sepcutoff.txt",
"GATKSVPipelineSingleSample.contig_ploidy_model_tar" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/gcnv_model/ref_panel_v1b-contig-ploidy-model.tar.gz",
"GATKSVPipelineSingleSample.ref_ped_file" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/ped/ref_panel_v1b.ped",
"GATKSVPipelineSingleSample.ref_panel_bincov_matrix": "gs://gatk-sv-resources/clinical/reference_panel_v1b/merged_evidence/ref_panel_v1b.bincov.bed.gz",
"GATKSVPipelineSingleSample.ref_panel_del_bed" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/merged_evidence/ref_panel_v1b.DEL.bed.gz",
"GATKSVPipelineSingleSample.ref_panel_dup_bed" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/merged_evidence/ref_panel_v1b.DUP.bed.gz",
"GATKSVPipelineSingleSample.ref_panel_outliers_excluded_list" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/post_filter/ref_panel_v1b.post03_outliers_excluded.samples.list",
"GATKSVPipelineSingleSample.ref_panel_outlier_samples_list" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/post_filter/ref_panel_v1b.post03_outliers.samples.list",
"GATKSVPipelineSingleSample.ref_panel_vcf" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/calls/ref_panel_v1b.cleaned.vcf.gz",
"GATKSVPipelineSingleSample.PE_metrics" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/genotyping/pe_metric_file.txt",
"GATKSVPipelineSingleSample.SR_metrics" : "gs://gatk-sv-resources/clinical/reference_panel_v1b/genotyping/sr_metric_file.txt",
"GATKSVPipelineSingleSample.bin_exclude": "gs://gatk-sv-resources/ref/bin_exclude.hg38.bed.gz",
"GATKSVPipelineSingleSample.cnmops_docker": "gatksv/cnmops:8645aa",
"GATKSVPipelineSingleSample.condense_counts_docker" : "gatksv/gatk:condensecounts-7396ae99aaab07e29c92b509a6515508fbe68158",
"GATKSVPipelineSingleSample.gatk_docker" : "broadinstitute/gatk:4.1.2.0",
"GATKSVPipelineSingleSample.genomes_in_the_cloud_docker" : "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.2-1510681135",
"GATKSVPipelineSingleSample.linux_docker" : "ubuntu:18.04",
"GATKSVPipelineSingleSample.manta_docker": "gatksv/manta:8645aa",
"GATKSVPipelineSingleSample.sv_base_docker": "gatksv/sv-base:cbb1fc",
"GATKSVPipelineSingleSample.sv_pipeline_base_docker": "mwalker174/sv-pipeline-base:mw-svtk-common-8d0ebd7",
"GATKSVPipelineSingleSample.sv_base_mini_docker": "gatksv/sv-base-mini:cbb1fc",
"GATKSVPipelineSingleSample.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_45c5354_single_sample_errors",
"GATKSVPipelineSingleSample.sv_pipeline_qc_docker": "gatksv/sv-pipeline-qc:cbb1fc",
"GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:cbb1fc",
"GATKSVPipelineSingleSample.wham_docker": "gatksv/wham:8645aa",
"GATKSVPipelineSingleSample.samtools_cloud_docker": "gatksv/samtools-cloud:8645aa",
"GATKSVPipelineSingleSample.allosome_file" : "gs://gatk-sv-resources/resources/allosome.fai",
"GATKSVPipelineSingleSample.cnmops_blacklist" : "gs://gatk-sv-resources/resources/GRCh38_Nmask.bed",
"GATKSVPipelineSingleSample.autosome_file" : "gs://gatk-sv-resources/resources/autosome.fai",
"GATKSVPipelineSingleSample.primary_contigs_list" : "gs://gatk-sv-resources/resources/primary_contigs.list",
"GATKSVPipelineSingleSample.primary_contigs_fai" : "gs://gatk-sv-resources/resources/contig.fai",
"GATKSVPipelineSingleSample.coverage_blacklist" : "gs://gatk-sv-resources/resources/GRCh38_Nmask.bed",
"GATKSVPipelineSingleSample.empty_file" : "gs://gatk-sv-resources/resources/empty.file",
"GATKSVPipelineSingleSample.genome_file" : "gs://gatk-sv-resources/resources/hg38.genome",
"GATKSVPipelineSingleSample.inclusion_bed" : "gs://gatk-sv-resources/resources/hg38_primary_contigs.bed",
"GATKSVPipelineSingleSample.max_ref_panel_carrier_freq": 0.03,
"GATKSVPipelineSingleSample.manta_region_bed" : "gs://gatk-sv-resources/resources/primary_contigs_plus_mito.bed.gz",
"GATKSVPipelineSingleSample.pesr_blacklist" : "gs://gatk-sv-resources/resources/PESR.enconde.peri_all.repeats.delly.hg38.blacklist.bed.gz",
"GATKSVPipelineSingleSample.ref_build" : "hg38",
"GATKSVPipelineSingleSample.reference_dict" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"GATKSVPipelineSingleSample.reference_fasta" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"GATKSVPipelineSingleSample.reference_index" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"GATKSVPipelineSingleSample.rmsk": "gs://gatk-sv-resources/resources/hg38.randomForest_blacklist.withRepMask.bed.gz",
"GATKSVPipelineSingleSample.segdups": "gs://gatk-sv-resources/resources/hg38.SD_gaps_Cen_Tel_Heter_Satellite_lumpy.blacklist.sorted.merged.bed.gz",
"GATKSVPipelineSingleSample.cytobands": "gs://gatk-sv-resources/resources/cytobands_hg38.bed.gz",
"GATKSVPipelineSingleSample.mei_bed": "gs://gatk-sv-resources/resources/mei_hg38.bed.gz",
"GATKSVPipelineSingleSample.pe_blacklist": "gs://gatk-sv-resources/resources/PESR.enconde.peri_all.repeats.delly.hg38.blacklist.bed.gz",
"GATKSVPipelineSingleSample.qc_definitions": "gs://gatk-sv-resources/clinical/reference_panel_v1b/qc/single_sample.qc_definitions.tsv",
"GATKSVPipelineSingleSample.depth_blacklist": "gs://gatk-sv-resources/resources/depth_blacklist.bed.gz",
"GATKSVPipelineSingleSample.wgd_scoring_mask" : "gs://gatk-sv-resources/resources/wgd_scoring_mask.hg38.gnomad_v3.bed",
"GATKSVPipelineSingleSample.wham_whitelist_bed_file": "gs://gatk-sv-resources/resources/wham_whitelist.bed",
"GATKSVPipelineSingleSample.depth_flags" : "--merge-coordinates",
"GATKSVPipelineSingleSample.depth_frac" : 0.8,
"GATKSVPipelineSingleSample.gcnv_qs_cutoff" : 30,
"GATKSVPipelineSingleSample.genotyping_n_per_split" : 1000,
"GATKSVPipelineSingleSample.matrix_qc_distance" : 1000000,
"GATKSVPipelineSingleSample.min_svsize" : 50,
"GATKSVPipelineSingleSample.n_RD_genotype_bins" : 100000,
"GATKSVPipelineSingleSample.pesr_distance" : 300,
"GATKSVPipelineSingleSample.pesr_flags" : "--preserve-ids",
"GATKSVPipelineSingleSample.pesr_frac" : 0.1,
"GATKSVPipelineSingleSample.pesr_svsize" : 0,
"GATKSVPipelineSingleSample.ref_copy_number_autosomal_contigs" : 2,
"GATKSVPipelineSingleSample.clean_vcf_min_sr_background_fail_batches": 0.5,
"GATKSVPipelineSingleSample.clean_vcf_max_shards_per_chrom" : 100,
"GATKSVPipelineSingleSample.clean_vcf_min_variants_per_shard" : 30,
"GATKSVPipelineSingleSample.clean_vcf_max_shards_per_chrom_clean_vcf_step1": 200,
"GATKSVPipelineSingleSample.clean_vcf_min_records_per_shard_clean_vcf_step1": 5000,
"GATKSVPipelineSingleSample.clean_vcf_samples_per_clean_vcf_step2_shard": 100,
"GATKSVPipelineSingleSample.clean_vcf_random_seed": 0,
"GATKSVPipelineSingleSample.clean_vcf_include_external_benchmarking": "false",
"GATKSVPipelineSingleSample.run_vcf_qc" : false,
"GATKSVPipelineSingleSample.ref_samples" : [
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"SM-BZNZR",
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"SM-BZNZV",
"SM-BZNZW",
"SM-BZO12",
"SM-BZO13",
"SM-BZO14",
"SM-BZO15",
"SM-BZO16",
"SM-BZO17",
"SM-BZO18",
"SM-BZO19",
"SM-BZO1A",
"SM-BZO1B",
"SM-BZO1C",
"SM-BZO1D",
"SM-BZO1E",
"SM-BZO1F",
"SM-G947I",
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"SM-G947V",
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"SM-GN4BG",
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"SM-GN4BJ",
"SM-GN5WW",
"SM-GN5WX",
"SM-GN5WY",
"SM-GN5WZ",
"SM-GN5X1",
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"SM-GZQK6",
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"SM-GZQLV",
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"SM-GZQM8",
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"SM-GZQPL",
"SM-GZQPX",
"SM-GZQQA",
"SM-GZQRA",
"SM-GZQRM",
"SM-GZQRY",
"TCGA-3C-AALJ-10A-01D-A702-36",
"TCGA-4C-A93U-10A-01D-A702-36",
"TCGA-4H-AAAK-10A-01D-A702-36",
"TCGA-93-A4JQ-10A-01D-A702-36",
"TCGA-A2-A4RX-10A-01D-A702-36",
"TCGA-BJ-A3PU-10A-01D-A703-36",
"TCGA-BR-A4J1-10A-01D-A703-36",
"TCGA-C8-A8HR-10A-01D-A703-36",
"TCGA-DB-A4XD-10A-01D-A704-36",
"TCGA-DB-A75K-10A-01D-A704-36",
"TCGA-DB-A75M-10A-01D-A704-36",
"TCGA-DU-A7TD-10A-01D-A704-36",
"TCGA-E1-A7YI-10A-01D-A704-36",
"TCGA-EJ-A46G-10A-01D-A704-36",
"TCGA-EJ-A65F-10A-01D-A704-36",
"TCGA-F6-A8O3-10A-01D-A704-36",
"TCGA-F6-A8O4-10A-01D-A704-36",
"TCGA-F9-A7VF-10A-01D-A704-36",
"TCGA-FG-A4MU-10A-01D-A705-36",
"TCGA-FG-A4MY-10A-01D-A705-36",
"TCGA-HE-A5NI-10A-01D-A705-36",
"TCGA-LN-A9FQ-10A-01D-A705-36",
"TCGA-MP-A4TC-10A-01D-A706-36",
"TCGA-P5-A72W-10A-01D-A706-36",
"TCGA-P5-A72X-10A-01D-A706-36",
"TCGA-P5-A735-10A-01D-A706-36",
"TCGA-P5-A736-10A-01D-A706-36",
"TCGA-P5-A77X-10A-01D-A706-36",
"TCGA-PL-A8LZ-10A-01D-A706-36",
"TCGA-S3-AA0Z-10A-01D-A706-36",
"TCGA-SS-A7HO-10A-01D-A703-36",
"TCGA-W9-A837-10A-01D-A706-36"
],
"GATKSVPipelineSingleSample.ref_std_manta_vcfs" : [
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"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_001.manta.SM-BZNZR.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_002.manta.SM-BZNZS.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_003.manta.SM-BZNZT.vcf.gz",
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"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_005.manta.SM-BZNZV.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_006.manta.SM-BZNZW.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_009.manta.SM-BZO12.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_010.manta.SM-BZO13.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_011.manta.SM-BZO14.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_012.manta.SM-BZO15.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_013.manta.SM-BZO16.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_014.manta.SM-BZO17.vcf.gz",
"gs://gatk-sv-resources/clinical/reference_panel_v1b/manta_std/std_015.manta.SM-BZO18.vcf.gz",
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