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(BP2.2) Calling Variants with UnifiedGenotyper [RETIRED]
This article is now obsolete as UnifiedGenotyper is no longer part of our recommended Best Practices workflow. It should only be used for calling variants on non-diploid organisms or pooled DNA samples. We are working on enabling HaplotypeCaller to handle non-diploid organisms, so hopefully it will replace UG in this aspect as well in the near future.
Although we generally recommend using the HaplotypeCaller for calling variants, in some cases it is not possible to do so, as explained in the FAQs. In those cases (i.e. when you're processing a high number of samples together, working with non-diploid organisms or with pooled samples) you should use the UnifiedGenotyper instead.
The Unified Genotyper calls SNPs and indels separately by considering each variant locus independently. The model it uses to do so has been generalized to work with data from organisms of any ploidy.