germline_fastqToVcf.example_inputs.json

{
  "sentieon_germline.r1_fastq": [
    "sentieon_quickstart/1.fastq.gz"
  ],
  "sentieon_germline.r2_fastq": [
    "sentieon_quickstart/2.fastq.gz"
  ],
  "sentieon_germline.read_groups": [
    "@RG\\tID:sample-1\\tSM:sample\\tPL:ILLUMINA"
  ],
  "sentieon_germline.ref_fasta": "sentieon_quickstart/reference/ucsc.hg19_chr22.fasta",
  "sentieon_germline.ref_fai": "sentieon_quickstart/reference/ucsc.hg19_chr22.fasta.fai",
  "sentieon_germline.ref_amb": "sentieon_quickstart/reference/ucsc.hg19_chr22.fasta.amb",
  "sentieon_germline.ref_ann": "sentieon_quickstart/reference/ucsc.hg19_chr22.fasta.ann",
  "sentieon_germline.ref_bwt": "sentieon_quickstart/reference/ucsc.hg19_chr22.fasta.bwt",
  "sentieon_germline.ref_pac": "sentieon_quickstart/reference/ucsc.hg19_chr22.fasta.pac",
  "sentieon_germline.ref_sa": "sentieon_quickstart/reference/ucsc.hg19_chr22.fasta.sa",
  "sentieon_germline.sentieon_license_server": "<licsrvr_fqdn>:<licsrvr_port>",
  "sentieon_germline.bqsr_vcfs": [
    "sentieon_quickstart/reference/1000G_phase1.snps.high_confidence.hg19_chr22.sites.vcf.gz",
    "sentieon_quickstart/reference/dbsnp_135.hg19_chr22.vcf.gz",
    "sentieon_quickstart/reference/Mills_and_1000G_gold_standard.indels.hg19_chr22.sites.vcf.gz"
  ],
  "sentieon_germline.bqsr_vcf_tbis": [
    "sentieon_quickstart/reference/1000G_phase1.snps.high_confidence.hg19_chr22.sites.vcf.gz.tbi",
    "sentieon_quickstart/reference/dbsnp_135.hg19_chr22.vcf.gz.tbi",
    "sentieon_quickstart/reference/Mills_and_1000G_gold_standard.indels.hg19_chr22.sites.vcf.gz.tbi"
  ],
  "sentieon_germline.dbsnp_vcf": "sentieon_quickstart/reference/dbsnp_135.hg19_chr22.vcf.gz",
  "sentieon_germline.dbsnp_vcf_tbi": "sentieon_quickstart/reference/dbsnp_135.hg19_chr22.vcf.gz.tbi",
  "sentieon_germline.sentieon_docker": "sentieon/sentieon-wdl:latest"
}