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.

Data Processing Pipeline

mike_boursnellmike_boursnell Posts: 69Member
edited August 2012 in Ask the team

Can the DataProcessingPipeline (as used by Queue.jar) be used to process BAM files in the best recommended way ("Best: multi-sample realignment with known sites and recalibration")

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