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GenotypeAndValidate doesn't work for SNPs

pdexheimerpdexheimer Member ✭✭✭✭
edited October 2012 in Ask the GATK team

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.

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