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In working with a mapping that has a very large coverage in certain places, I have noticed that the Unified Genotyper often calls SNPs even if the alternate allele is only present in a minuscule <1% fraction of the reads at a position. It is difficult to filter these SNPs out because QUAL is high for these SNPs the and QD, which is low in these situations, is also low for many other (good) SNPs.
There already is a fractional threshold option for indel calling, -minIndelFrac. Is there any similar option for SNPs – and if not, what is your reasoning for omitting this option and what steps do you recommend for filtering out these SNPs?