allParams.haplotag.ont-r94g507.hp.json

{
        "include" : "../base_params.json",
        "polish": {
                "filterAlignmentsWithMapQBelowThisThreshold": 5,
                "maxDepth": 32
        },
        "phase" : {
                "onlyUseSNPVCFEntries": false,
                "useVariantSelectionAdaptiveSampling": true,
                "variantSelectionAdaptiveSamplingPrimaryThreshold": 15,
                "variantSelectionAdaptiveSamplingDesiredBasepairsPerVariant": 2000,
                "minSnpVariantQuality": 5,
                "minIndelVariantQuality": 20
        }
}