etc/gatk-wdl/FullSomaticPipeline.json

   1 {
   2   "##_COMMENT1": "Take note of the .64 extensions on the reference files, issues between 32 and 64 bit OS",
   3
   4   "##_COMMENT2": "SAMPLE NAME AND UNMAPPED BAMS",
   5   "FullSomaticPipeline.tumor_base_file_name": "HCC1143T",
   6   "FullSomaticPipeline.tumor_flowcell_unmapped_bams": [
   7       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0ENM.1.unmapped.bam",
   8       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0ENM.2.unmapped.bam",
   9       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0ENM.3.unmapped.bam",
  10       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0ENM.5.unmapped.bam",
  11       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0ENM.6.unmapped.bam",
  12       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0ENM.7.unmapped.bam",
  13       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0UK2.4.unmapped.bam",
  14       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0UK2.8.unmapped.bam",
  15       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0UW5.4.unmapped.bam",
  16       "gs://gatk-test-data/wgs_ubam/HCC1143T/D0UW5.8.unmapped.bam"
  17   ],
  18   "FullSomaticPipeline.normal_base_file_name": "HCC1143BL",
  19   "FullSomaticPipeline.normal_flowcell_unmapped_bams": [
  20      "gs://gatk-test-data/wgs_ubam/HCC1143BL/C09DF.1.unmapped.bam",
  21      "gs://gatk-test-data/wgs_ubam/HCC1143BL/C09DF.2.unmapped.bam",
  22      "gs://gatk-test-data/wgs_ubam/HCC1143BL/D0EN0.4.unmapped.bam",
  23      "gs://gatk-test-data/wgs_ubam/HCC1143BL/D0EN0.7.unmapped.bam",
  24      "gs://gatk-test-data/wgs_ubam/HCC1143BL/D0EN0.8.unmapped.bam",
  25      "gs://gatk-test-data/wgs_ubam/HCC1143BL/D0UK2.1.unmapped.bam",
  26      "gs://gatk-test-data/wgs_ubam/HCC1143BL/D0UK2.2.unmapped.bam",
  27      "gs://gatk-test-data/wgs_ubam/HCC1143BL/D0UK2.6.unmapped.bam",
  28      "gs://gatk-test-data/wgs_ubam/HCC1143BL/D0UK2.7.unmapped.bam"
  29   ],
  30   "FullSomaticPipeline.unmapped_bam_suffix": ".bam",
  31
  32   "##_COMMENT3": "REFERENCES",
  33   "FullSomaticPipeline.fingerprint_genotypes_file": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf",
  34   "FullSomaticPipeline.contamination_sites_ud": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.contam.UD",
  35   "FullSomaticPipeline.contamination_sites_bed": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.contam.bed",
  36   "FullSomaticPipeline.contamination_sites_mu": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.contam.mu",
  37   "FullSomaticPipeline.wgs_calling_interval_list": "gs://broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
  38   "FullSomaticPipeline.ref_dict": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
  39   "FullSomaticPipeline.ref_fasta": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
  40   "FullSomaticPipeline.ref_fasta_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
  41   "FullSomaticPipeline.ref_alt": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
  42   "FullSomaticPipeline.ref_sa": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
  43   "FullSomaticPipeline.ref_amb": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
  44   "FullSomaticPipeline.ref_bwt": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
  45   "FullSomaticPipeline.ref_ann": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
  46   "FullSomaticPipeline.ref_pac": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
  47   "FullSomaticPipeline.known_indels_sites_VCFs": [
  48     "gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
  49     "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
  50   ],
  51   "FullSomaticPipeline.known_indels_sites_indices": [
  52     "gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
  53     "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
  54   ],
  55   "FullSomaticPipeline.dbSNP_vcf": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
  56   "FullSomaticPipeline.dbSNP_vcf_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
  57   "FullSomaticPipeline.wgs_coverage_interval_list": "gs://broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list",
  58
  59   "##_COMMENT4": "PRIVATE REFERENCES",
  60
  61   "##_COMMENT5": "DISK SIZES + MISC",
  62   "FullSomaticPipeline.flowcell_small_disk": 100,
  63   "FullSomaticPipeline.flowcell_medium_disk": 200,
  64   "FullSomaticPipeline.agg_small_disk": 200,
  65   "FullSomaticPipeline.agg_medium_disk": 300,
  66   "FullSomaticPipeline.agg_large_disk": 400,
  67   "FullSomaticPipeline.preemptible_tries": 0,
  68   "FullSomaticPipeline.agg_preemptible_tries": 0,
  69
  70   "##_COMMENT6": "SOMATIC PIPELINES (M2 & CNV)",
  71   "FullSomaticPipeline.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.0.1.2",
  72   "FullSomaticPipeline.is_run_oncotator": true,
  73
  74   "##_COMMENT7": "SOMATIC PIPELINES (CNV only)",
  75   "FullSomaticPipeline.common_sites": "gs://gatk-test-data/cnv/somatic/somatic-hg38_af-only-gnomad.hg38.AFgt0.02.interval_list",
  76   "FullSomaticPipeline.bin_length": 250,
  77   "FullSomaticPipeline.read_count_pon": "gs://gatk-test-data/cnv/somatic/PoN_4.0_WGS_for_public.pon.hdf5",
  78   "FullSomaticPipeline.mem_gb_for_model_segments": 31,
  79
  80   "##_COMMENT8": "SOMATIC PIPELINES (M2 only)",
  81   "FullSomaticPipeline.artifact_modes": ["G/T", "C/T"],
  82   "FullSomaticPipeline.gnomad": "gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz",
  83   "FullSomaticPipeline.gnomad_index": "gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz.tbi",
  84   "FullSomaticPipeline.is_bamOut": false,
  85   "FullSomaticPipeline.is_run_orientation_bias_filter": true,
  86   "FullSomaticPipeline.pon": "gs://gatk-test-data/mutect2/M2PoN_4.0_WGS_for_public.vcf",
  87   "FullSomaticPipeline.pon_index": "gs://gatk-test-data/mutect2/M2PoN_4.0_WGS_for_public.vcf.idx",
  88   "FullSomaticPipeline.scatter_count": 30,
  89   "FullSomaticPipeline.variants_for_contamination": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz",
  90   "FullSomaticPipeline.variants_for_contamination_index": "gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz.tbi"
  91 }
  92