Multisample_Fastq_to_Gvcf_GATK4_inputs_hg38.json

{
  "##_COMMENT1": "SAMPLES",
  "Multisample_Fastq_to_Gvcf_GATK4.inputSamplesFile": "samples.txt",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_name": "hg38",
  "Multisample_Fastq_to_Gvcf_GATK4.unmapped_bam_suffix": ".bam",

  "##_COMMENT2": "REFERENCE FILES",
  "Multisample_Fastq_to_Gvcf_GATK4.scattered_calling_intervals_list": "/data/hg38/v0/hg38_wgs_scattered_calling_intervals.txt", 
  "Multisample_Fastq_to_Gvcf_GATK4.ref_dict": "/data/hg38/v0/Homo_sapiens_assembly38.dict",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_fasta": "/data/hg38/v0/Homo_sapiens_assembly38.fasta",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_fasta_index": "/data/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_alt": "/data/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_sa": "/data/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_amb": "/data/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_bwt": "/data/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_ann": "/data/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
  "Multisample_Fastq_to_Gvcf_GATK4.ref_pac": "/data/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
  
  "##_COMMENT3": "KNOWN SITES RESOURCES", 
  "Multisample_Fastq_to_Gvcf_GATK4.dbSNP_vcf": "/data/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
  "Multisample_Fastq_to_Gvcf_GATK4.dbSNP_vcf_index": "/data/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
  "Multisample_Fastq_to_Gvcf_GATK4.known_indels_sites_VCFs": [
    "/data/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
    "/data/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
  ],
  "Multisample_Fastq_to_Gvcf_GATK4.known_indels_sites_indices": [
    "/data/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
    "/data/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
  ],

  "##_COMMENT4": "MISC PROGRAM PARAMETERS", 
  "Multisample_Fastq_to_Gvcf_GATK4.bwa_commandline": "bwa mem -p -v 3 -t 16 -Y $bash_ref_fasta",
  "Multisample_Fastq_to_Gvcf_GATK4.compression_level": 2
}