panelCapture_example_inputs.json

{
  "panelCapture.sampleID": "ERR1341793",
  "panelCapture.suffix1": "_1",
  "panelCapture.suffix2": "_2",
  "panelCapture.suffixIndex": "",
  "panelCapture.suffixIndex2": "",
  "panelCapture.fastqR1": "/Path/to/Syndip/fastqs/ERR1341793_1.fastq.gz",
  "panelCapture.fastqR2": "/Path/to/Syndip/fastqs/ERR1341793_2.fastq.gz",
  "panelCapture.platform": "ILLUMINA",
  "panelCapture.genomeVersion": "hg19",
  "panelCapture.workflowType": "panelCapture",
  "panelCapture.intervalBedFile": "/Path/to/bedfile.bed",
  "panelCapture.outDir": "/Path/to/tmp_output/",
  "panelCapture.bedtoolsLowCoverage": "20",
  "panelCapture.bedToolsSmallInterval": "20",
  "panelCapture.cpuLow": "1",
  "panelCapture.cpuHigh": "24",
  "panelCapture.memoryLow": "2500",
  "panelCapture.memoryHigh": "12000",
  "panelCapture.javaRam": "6",
  "panelCapture.refFasta": "/Path/to/hg19.fa",
  "panelCapture.refFai": "/Path/to/hg19.fa.fai",
  "panelCapture.refDict": "/Path/to/hg19.dict",
  "panelCapture.refBwt": "/Path/to/hg19.fa.bwt",
  "panelCapture.refAnn": "/Path/to/hg19.fa.ann",
  "panelCapture.refPac": "/Path/to/hg19.fa.pac",
  "panelCapture.refSa": "/Path/to/hg19.fa.sa",
  "panelCapture.refAmb": "/Path/to/hg19.fa.amb",
  "panelCapture.knownSites1": "/Path/to/1000G_phase1.indels.hg19.sites.vcf.gz",
  "panelCapture.knownSites1Index": "/Path/to/1000G_phase1.indels.hg19.sites.vcf.gz.tbi",
  "panelCapture.knownSites2": "/Path/to/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz",
  "panelCapture.knownSites2Index": "/Path/to/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz.tbi",
  "panelCapture.knownSites3": "/Path/to/dbsnp.hg19.vcf.gz",
  "panelCapture.knownSites3Index": "/Path/to/dbsnp.hg19.vcf.gz.tbi",
  "panelCapture.refFastaGz": "/Path/to/hg19.fa.gz",
  "panelCapture.refFaiGz": "/Path/to/hg19.fa.gz.fai",
  "panelCapture.refFaiGzi": "/Path/to/hg19.fa.gz.gzi",
  "panelCapture.samtoolsExe": "/Path/to/samtools",
  "panelCapture.awkExe": "/Path/to/awk",
  "panelCapture.sedExe" : "/Path/to/sed",
  "panelCapture.sortExe": "/Path/to/sort",
  "panelCapture.javaExe": "/Path/to/java",
  "panelCapture.rtgExe":"/Path/to/rtg-tools-3.10.1/rtg",
  "panelCapture.vcftoolsExe" :"/Path/to/vcftools",
  "panelCapture.bgZipExe": "/Path/to/bgzip",
  "panelCapture.tabixExe": "/Path/to/tabix",
  "panelCapture.fastqcExe": "/Path/to/fastqc",
  "panelCapture.bwaExe": "/Path/to/bwa",
  "panelCapture.sambambaExe": "/Path/to/sambamba",
  "panelCapture.bedToolsExe": "/Path/to/bedtools",
  "panelCapture.crumbleExe": "/Path/to/crumble",
  "panelCapture.ldLibraryPath": "/usr/local/lib",
  "panelCapture.gatkExe": "/Path/to/gatkexe",
  "panelCapture.gatk3Jar": "/Path/to/gatk3.jar",
  "panelCapture.qualimapExe": "/Path/to/qualimap",
  "panelCapture.vcfPolyXJar": "/Path/to//jvarkit/dist/vcfpolyx.jar",
  "panelCapture.bcfToolsExe": "/Path/to/bcftools",
  "panelCapture.multiqcExe": "/Path/to/multiqc",
  "panelCapture.subdivisionMode": "BALANCING_WITHOUT_INTERVAL_SUBDIVISION",
  "panelCapture.minCovBamQual": "30",
  "panelCapture.swMode": "FASTEST_AVAILABLE",
  "panelCapture.vcfHcSuffix": ".raw",
  "panelCapture.vcfSISuffix": ".merged",
  "panelCapture.mergeVCFMobiDL": "/Path/to/anacoreUtilsMergeVCFCallersMobiDL.py",
  "panelCapture.dvOut" : "/dv2/tmp_output",
  "panelCapture.refData": "/Path/to/refData/:/dv2/refData/",
  "panelCapture.data": "/Actual/path/to/data:/dv2/data",
  "panelCapture.bedFile": "/dv2/refData/intervals/func.37m.chr.awked.bed",
  "panelCapture.deepExe": "/opt/deepvariant/bin/run_deepvariant",
  "panelCapture.outputMnt": "/softs/MobiDL/tmp_output:/dv2/tmp_output",
  "panelCapture.singularity": "/Path/to/singularity",
  "panelCapture.modelType": "WES",
  "panelCapture.singularityImg": "/Path/to/deepvariant-custom.simg",
  "panelCapture.referenceFasta": "/dv2/refData/genome/hg19/hg19.fa"
}