Mark DePristo 35139cf990 HaplotypeScore only annotates SNPs ... -- The new HMM new edge conditions the likelihoods are offset by log10(n possible starts) so the results don't really mean "fits the haplotype well" any longer. This results in grossly inflated HaplotypeScores for indels and with the HaplotypeCaller. So I'm simply not going to emit this annotation value any longer for indels and for the HC		2013-02-09 19:19:28 -05:00
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java	HaplotypeScore only annotates SNPs	2013-02-09 19:19:28 -05:00