Laura Gauthier 9f3cbb2ef1 Improvements to CalculateGenotypePosteriors and CalibrateGenotypeLikelihoods ... CalculateGenotypePosteriors now only computes posterior probs for SNP sites with SNP priors (other sites have flat priors applied) CalibrateGenotypeLikelihoods had originally applied HOM_REF/HET/HOM_VAR frequencies in callset as priors before empirical quality analysis. Now has option (-noPriors) to not apply/apply flat priors. Also takes in new external probabilities files, such as those generated by CGP, from which the genotype posterior probability qualities will be read. Integration test was changed to account for new SNP-only behavior and default behavior to not use missing priors. (Also, new numRefIfMissing is 0, which should only matter in cases using few samples when you probably don't want to be doing that anyway!)		2014-04-24 08:49:42 -04:00
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gatk-protected	Improvements to CalculateGenotypePosteriors and CalibrateGenotypeLikelihoods	2014-04-24 08:49:42 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.2 development	2014-03-18 01:18:59 -04:00