{
  "makeRegions": {
    "slop": "250",
    "minCoverage": "10",
    "maxCoverage": "200",
    "maxRegionLength": "100000",
    "minRepeatPeriod": "6",
    "minRepeatLength": "100",
    "functionalRegions": "none",
    "genomeBuild": "hg38",
    "overlappedFunctionalRegions": "false",
    "ucscTable": "simpleRepeat",
    "minRepeatFunctionalOverlap": "1"
  },
  "makeCalls": {
    "singleBaseMatchReward": "10",
    "singleBaseMismatchPenalty": "12",
    "gapOpenPenalties": "10,35",
    "gapExtensionPenalties": "1,0",
    "minUnitigMappingQuality": "1"
  },
  "filterCalls": {
    "maxIntraClusterDistance": "500",
    "minSVSize": "50",
    "minUnitigMappingQuality": "0",
    "minUnitigBlockLength": "40"
  }
}