I'm looking to find all the entries that change between two calls to UG on the same data. I would like to find all the entries where the call in the variant tract are different from those in the comparison track. So in effect I want those entries that would not be result from -using -conc in SelectVariants. From the documentation is is unclear if the -disc option does this:
A site is considered discordant if there exists some sample in the variant track that has a non-reference genotype and either the site isn't present in this track, the sample isn't present in this track, or the sample is called reference in this track.
What if the comp is HOM_VAR and the variant track is HET? Or if they are both HET but disagree on the specific allele?