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The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, and its ability to call indels is far superior. We recommend using HaplotypeCaller in all cases, with only a few exceptions:
In those cases, we recommend using UnifiedGenotyper instead of HaplotypeCaller.
Geraldine Van der Auwera, PhD