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multiple alleles in a diploid genome
When running UnifiedGenotyper (GATK 2.3-9), I checked the running log, and kept seeing the warning message: "DiploidExactAFCalc - this tool is currently set to genotype at most 3 alternate alleles in a given context...."
I set max alternate alleles to be 3 here. However, I remember that this information was minimal (or even none) when I run GATK 1.6.5 on the same dataset. Do I need to take any caution on these warning messages? You can see the attached figure that this information is a lot during a complete run... just a bit worry if the real alternate alleles will be picked up if the program sees multiple alleles on the same locus.