MuTect: best somatic mutation caller

Appistry: Which caller (Haplotype Caller or Unified Genotyper) would be best practice for somatic mutation calling?

Neither, as the GATK is not tuned to discover low allelic fraction mutations. The better option is to use Appistry’s Cancer Genome Analysis Suite, which contains MuTect. MuTect is specifically designed to discover somatic mutations.

Appistry: How about the mitochondrial sequence in a diploid genome?

This should be possible using the ploidy settings in the Haplotype Caller now, but we do not have any recommendations to share with you on this. Of course, if you do experiment with this, you would need to call the MT chromosomes separately, as using ploidy settings over the whole human diploid genome would result in a very high number of false positive calls. To limit your calls to the MT, you would use a –L MT (b37 reference) or a –L chrM (hg19) and add an appropriate ploidy value –ploidy 4 for example.