diff --git a/python/snpSelector.py b/python/snpSelector.py index 585c52195..b7db252cc 100755 --- a/python/snpSelector.py +++ b/python/snpSelector.py @@ -123,7 +123,7 @@ def titvFPRateEstimate(variants, target): # gaussian model def gaussianModel(): LEFT_HANDED = True - sigma = 5 + sigma = 1 # old value is 5 constant = 1 / math.sqrt(2 * math.pi * sigma**2) exponent = -1 * ( titvRatio - target )**2 / (2 * sigma**2) TPRate = gaussian(titvRatio, target, sigma) / gaussian(target, target, sigma) @@ -133,12 +133,8 @@ def titvFPRateEstimate(variants, target): if DEBUG: print 'TPRate', TPRate, constant, exponent, dephredScale(OPTIONS.maxQScore) return TPRate - #denom = (0.2 - 0.8 * titvRatio) - #FPRate = 1 - #if denom <> 0: - # FPRate = (1.0 / (target+1)) * (titvRatio - target) / denom - - FPRate = 1 - gaussianModel() + FPRate = 1 - theoreticalCalc() + #FPRate = 1 - gaussianModel() nVariants = len(variants) if DEBUG: print ':::', nVariants, titvRatio, target, FPRate @@ -426,7 +422,7 @@ def setup(): type='int', default=None, help="Maximum number of input VCF records to process, if provided. Default is all records") parser.add_option("-q", "--qMax", dest="maxQScore", - type='int', default=30, + type='int', default=60, help="The maximum Q score allowed for both a single covariate and the overall QUAL score [default: %default]") parser.add_option("-o", "--outputVCF", dest="outputVCF", type='string', default=None,