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.

HaplotypeCaller and Reduced BAMs

fadistafadista Posts: 3Member
edited August 2012 in Ask the team

Hi,

I would like to ask if the most recent version of GATK is stable enough for HaplotypeCaller to work well with Reduced BAMs. If not, can you give an estimate of when would that be in place? Thanks in advance.

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