GenotypeAndValidate doesn't work for SNPs
When I run GenotypeAndValidate, all of the SNPs in my gold standard VCF get lumped into the "not confident" category. When I run UnifiedGenotyper over the same samples in DISCOVERY mode, these same SNPs have QUAL scores in the thousands.
I think the problem is in the creation of the UnifiedGenotyperEngines in GenotypeAndValidate.java (lines 335-340). The same UnifiedArgumentCollection is given to the constructors of both snpEngine and indelEngine, with the GLmodel field changed. But since each engine has a reference to the same structure, they both ultimately see the GLmodel that is set last (indel).
I'm sorry to not include a patch, I don't have local compilation set up right now.