captainAchab_example_inputs.json

{
  "captainAchab.sampleID": "SampleID",
  "captainAchab.inputVcf": "/Path/to/SampleID/SampleID.vcf",
  "captainAchab.newHope": true,
  "captainAchab.withPhenolyzer":true,
  "captainAchab.diseaseFile": "/Path/to/SampleID/disease.txt",
  "captainAchab.checkTrio": "",
  "captainAchab.caseSample": "",
  "captainAchab.fatherSample": "",
  "captainAchab.motherSample": "",
  "captainAchab.genesOfInterest": "",
  "captainAchab.filterList":"",
  "captainAchab.cnvGeneList":"",
  "captainAchab.workflowType":"CaptainAchab", 
  "captainAchab.outDir": "/Path/to/outdir/",
  "captainAchab.allelicFrequency": 0.01,
  "captainAchab.mozaicRate":0.2,
  "captainAchab.mozaicDP":5,
  "captainAchab.customInfo": "",
  "captainAchab.customVCF": "",
  "captainAchab.affected": "",
  "captainAchab.favouriteGeneRef": "",
  "captainAchab.filterCustomVCF": "",
  "captainAchab.filterCustomVCFRegex": "",
  "captainAchab.keepFiles":false,
  "captainAchab.cpu":"1", 
  "captainAchab.memory":"4000", 
  "captainAchab.humanDb": "/Path/to/annovar/humandb",
  "captainAchab.customXref": "/Path/to/annovar/humandb/gene_customfullxref.txt",
  "captainAchab.fastaGenome":"/Path/to/genome/hg19/hg19.fa",
  "captainAchab.phenolyzerExe": "/Path/to/phenolyzer",
  "captainAchab.mpaExe": "/Path/to/mpa",
  "captainAchab.tableAnnovarExe": "/Path/to/annovar/2018Apr06/table_annovar.pl",
  "captainAchab.achabExe": "/Path/to/Captain-ACHAB/achab.pl",
  "captainAchab.refAnnotateVariation":"/Path/to/annovar/2018Apr06/annotate_variation.pl",
  "captainAchab.refCodingChange":"/Path/to/annovar/2018Apr06/coding_change.pl",
  "captainAchab.refConvert2Annovar":"/Path/to/annovar/2018Apr06/convert2annovar.pl",
  "captainAchab.refRetrieveSeqFromFasta":"/Path/to/annovar/2018Apr06/retrieve_seq_from_fasta.pl",
  "captainAchab.refVariantsReduction":"/Path/to/annovar/2018Apr06/variants_reduction.pl",
  "captainAchab.gatkExe":"/Path/to/gatk",
  "captainAchab.bcftoolsExe":"/Path/to/bcftools",
  "captainAchab.perlPath":"/Path/to/perl",
  "captainAchab.pythonPath":"/Path/to/python3",
  "write_to_cache": true,
  "read_from_cache": true,
  "captainAchab.genome": "hg19",
  "captainAchab.annovarForMpa.CpuHigh": "4",
  "captainAchab.annovarForMpa.Clinvar": "clinvar_20190305",
  "captainAchab.annovarForMpa.Dbnsfp": "dbnsfp35a",
  "captainAchab.annovarForMpa.Spidex": "spidex",
  "captainAchab.annovarForMpa.Dbscsnv": "dbscsnv11",
  "captainAchab.annovarForMpa.GnomadExome": "gnomad_exome",
  "captainAchab.annovarForMpa.GnomadGenome": "gnomad_genome",
  "captainAchab.annovarForMpa.PopFreqMax": "popfreq_max_20150413",
  "captainAchab.annovarForMpa.Intervar": "intervar_20180118",
  "captainAchab.annovarForMpa.SpliceAI": "spliceai_filtered"
}