internal helper function to create Filt_Genotype column. note this column name is from Daniel's original BSA analysis. It just means a column which calls genotype based on frequency of allele with RealDepth, which are only those bases which pass the variant caller thresholds and exist (not missing in the CIGAR), in the denominator. Currently the three levels that may be returned are lowDepth, Rerence or Alterantive.
Arguments
- depth
depth of a given variant, at a given position
- ref_freq
frequency of a given variant, at a given position
- depth_thres
if less than depth threshold, or is.na(depth), return value is lowDepth
- ref_freq_thres
if ref is greater than or equal to this number, and depth passes threshold, call genotype Reference. note that genotype is called Alternative if passes depth threshold and ref_freq is less than or equal to 1 - ref_freq_thres. If depth is below depth_thres, return lowDepth