etc/gatk-wdl/germline2-joint-discovery-gatk4-local.hg38.wgs.inputs.json

   1 {
   2   "##_COMMENT1": "INPUT GVCFs & COHORT -- DATASET-SPECIFC, MUST BE ADAPTED",
   3   "JointGenotyping.sample_names": ["WGS-D3B","WGS-Normal"],
   4   "JointGenotyping.input_gvcfs": ["/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-D3B.hg38.g.vcf.gz","/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-Normal.hg38.g.vcf.gz"],
   5   "JointGenotyping.input_gvcfs_indices": ["/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-D3B.hg38.g.vcf.gz.tbi","/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-Normal.hg38.g.vcf.gz.tbi"],
   6   "JointGenotyping.callset_name": "NSFCwgs",
   7
   8   "##_COMMENT2": "REFERENCE FILES",
   9   "JointGenotyping.ref_fasta": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
  10   "JointGenotyping.ref_fasta_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
  11   "JointGenotyping.ref_dict": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
  12
  13   "##_COMMENT3": "INTERVALS",
  14   "JointGenotyping.eval_interval_list": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
  15   "JointGenotyping.unpadded_intervals_file": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
  16
  17   "##_COMMENT4": "RESOURCE FILES",
  18   "JointGenotyping.dbsnp_vcf": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
  19   "JointGenotyping.dbsnp_vcf_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
  20   "JointGenotyping.one_thousand_genomes_resource_vcf": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
  21   "JointGenotyping.one_thousand_genomes_resource_vcf_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
  22   "JointGenotyping.omni_resource_vcf": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
  23   "JointGenotyping.omni_resource_vcf_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi",
  24   "JointGenotyping.mills_resource_vcf": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
  25   "JointGenotyping.mills_resource_vcf_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
  26   "JointGenotyping.axiomPoly_resource_vcf": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz",
  27   "JointGenotyping.axiomPoly_resource_vcf_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi",
  28   "JointGenotyping.hapmap_resource_vcf": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
  29   "JointGenotyping.hapmap_resource_vcf_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi",
  30
  31   "##_COMMENT5": "VQSR PARAMETERS",
  32   "JointGenotyping.SNP_VQSR_downsampleFactor": 10,
  33   "JointGenotyping.snp_filter_level": 99.7,
  34   "JointGenotyping.indel_filter_level": 99.7,
  35   "JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"],
  36   "JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
  37   "JointGenotyping.snp_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.8", "99.6", "99.5", "99.4", "99.3", "99.0", "98.0", "97.0", "90.0" ],
  38   "JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"],
  39
  40   "##_COMMENT4": "DOCKERS",
  41   "JointGenotyping.python_docker": "python:2.7",
  42   "JointGenotyping.gatk_docker": "broadinstitute/gatk:4.0.6.0",
  43
  44   "##_COMMENT5": "PATHS",
  45   "JointGenotyping.gatk_path": "gatk",
  46
  47   "##_COMMENT8": "DISK SIZE ALLOCATION",
  48   "JointGenotyping.small_disk": 100,
  49   "JointGenotyping.medium_disk": 200,
  50   "JointGenotyping.large_disk": 300,
  51   "JointGenotyping.huge_disk": 400
  52 }