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Dear Geraldine, I have uploaded pairHmm_bug_bulasha.tar.gz to your FTP server. Hope you will be able to reproduce the bug and understand the reason of it. Thank you in advance.
Hi, Geraldine, i just tried HaplotypeCaller from the latest nightly build and received the same error ERROR MESSAGE: PairHMM Log Probability cannot be greater than 0: haplotype: [84, 84, 84, 65, 84, 84, 65, 65, 71, 71, 84, 84, 84, 84, 84, 84, 84, 8…
It was claimed here http://www.broadinstitute.org/gatk/guide/article?id=2572 for version 2.5: "Fixed problem where our internal PairHMM was generating positive likelihoods."
Hi, Geraldine, i have encountered the same error with HaplotypeCaller GenomeAnalysisTK-2.7-4-g6f46d11 and would like to know whether this problem was fixed.