etc/gatk-wdl/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json

   1 {
   2   "##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS",
   3   "PreProcessingForVariantDiscovery_GATK4.sample_name": "WGS-D3B",
   4   "PreProcessingForVariantDiscovery_GATK4.ref_name": "hg38",
   5   "PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-D3B_unmapped_bam.list",
   6   "PreProcessingForVariantDiscovery_GATK4.unmapped_bam_suffix": ".bam",
   7
   8   "##_COMMENT2": "REFERENCE FILES",
   9   "PreProcessingForVariantDiscovery_GATK4.ref_dict": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.dict",
  10   "PreProcessingForVariantDiscovery_GATK4.ref_fasta": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta",
  11   "PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.fai",
  12   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_alt": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.64.alt",
  13   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_sa": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.64.sa",
  14   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_amb": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.64.amb",
  15   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_bwt": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.64.bwt",
  16   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_ann": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.64.ann",
  17   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_pac": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.64.pac",
  18
  19   "##_COMMENT3": "KNOWN SITES RESOURCES",
  20   "PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.dbsnp138.vcf",
  21   "PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
  22   "PreProcessingForVariantDiscovery_GATK4.known_indels_sites_VCFs": [
  23     "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
  24     "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz"
  25   ],
  26   "PreProcessingForVariantDiscovery_GATK4.known_indels_sites_indices": [
  27     "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
  28     "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
  29   ],
  30
  31   "##_COMMENT4": "MISC PARAMETERS",
  32   "PreProcessingForVariantDiscovery_GATK4.bwa_commandline": "bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta",
  33   "PreProcessingForVariantDiscovery_GATK4.compression_level": 5,
  34   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.num_cpu": "16",
  35
  36   "##_COMMENT5": "DOCKERS",
  37   "PreProcessingForVariantDiscovery_GATK4.gotc_docker": "broadinstitute/genomes-in-the-cloud:2.3.1-1512499786",
  38   "PreProcessingForVariantDiscovery_GATK4.gatk_docker": "broadinstitute/gatk:4.0.4.0",
  39   "PreProcessingForVariantDiscovery_GATK4.python_docker": "python:2.7",
  40
  41   "##_COMMENT6": "PATHS",
  42   "PreProcessingForVariantDiscovery_GATK4.bwa_path": "/share/FGI2017B/brew/bin/",
  43   "PreProcessingForVariantDiscovery_GATK4.gotc_path": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/",
  44   "PreProcessingForVariantDiscovery_GATK4.gatk_path": "/share/FGI2017B/brew/bin/gatk",
  45
  46   "##_COMMENT7": "JAVA OPTIONS",
  47   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.java_opt": "-Xms3000m",
  48   "PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment.java_opt": "-Xms3000m",
  49   "PreProcessingForVariantDiscovery_GATK4.MarkDuplicates.java_opt": "-Xms4000m",
  50   "PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.java_opt_sort": "-Xms4000m",
  51   "PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.java_opt_fix": "-Xms500m",
  52   "PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator.java_opt": "-Xms4000m",
  53   "PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports.java_opt": "-Xms3000m",
  54   "PreProcessingForVariantDiscovery_GATK4.ApplyBQSR.java_opt": "-Xms3000m",
  55   "PreProcessingForVariantDiscovery_GATK4.GatherBamFiles.java_opt": "-Xms2000m",
  56
  57   "##_COMMENT8": "MEMORY ALLOCATION",
  58   "PreProcessingForVariantDiscovery_GATK4.GetBwaVersion.mem_size": "1 GB",
  59   "PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.mem_size": "14 GB",
  60   "PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment.mem_size": "3500 MB",
  61   "PreProcessingForVariantDiscovery_GATK4.MarkDuplicates.mem_size": "7 GB",
  62   "PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.mem_size": "5000 MB",
  63   "PreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV.mem_size": "2 GB",
  64   "PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator.mem_size": "6 GB",
  65   "PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports.mem_size": "3500 MB",
  66   "PreProcessingForVariantDiscovery_GATK4.ApplyBQSR.mem_size": "3500 MB",
  67   "PreProcessingForVariantDiscovery_GATK4.GatherBamFiles.mem_size": "3 GB",
  68
  69   "##_COMMENT9": "DISK SIZE ALLOCATION",
  70   "PreProcessingForVariantDiscovery_GATK4.agg_small_disk": 200,
  71   "PreProcessingForVariantDiscovery_GATK4.agg_medium_disk": 300,
  72   "PreProcessingForVariantDiscovery_GATK4.agg_large_disk": 400,
  73   "PreProcessingForVariantDiscovery_GATK4.flowcell_small_disk": 100,
  74   "PreProcessingForVariantDiscovery_GATK4.flowcell_medium_disk": 200,
  75
  76   "##_COMMENT10": "PREEMPTIBLES",
  77   "PreProcessingForVariantDiscovery_GATK4.preemptible_tries": 3,
  78   "PreProcessingForVariantDiscovery_GATK4.agg_preemptible_tries": 3
  79 }