Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Bug in HaplotypeCaller 2.4-7 : "Bad likelihoods detected"

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,293Administrator, GSA Member admin
edited March 2013 in Announcements

As reported here:
http://gatkforums.broadinstitute.org/discussion/comment/4114#Comment_4114

If you encounter this bug too, please don't post a new question about it. Feel free to comment in this thread to let us know you have also had the same problem.

Thank you for your patience while we work to fix this issue.

Update: the "Bad likelihoods detected error" is fixed in the latest version.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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