Increasing Window Size for HaplotypeScore Calculation
I am calling variants from reads mapped to scaffolds of a "closely distant" species (wild plant vs cultivated), however, I am having issues with sites that fall in paralogous sequences (More than two segregating haplotypes observed in the alignment). I read on here that the window size for calculating the HaplotypeScore is 21 basepairs (10 either side the marker of interest). Is there anyway to increase the size of that window? That haplotype score has been a useful resource for me in the refinement of my variant set, yet there remain erroneous sites. I have also done extensive read filtering prior to calling variants (removing reads tagged with bwa mem's XA, MQ > 50, read depth filtering).
If there is a way to increase the window size, that would help me out immensely.