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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.
Hi - unfortunately with the current 2.0.x version of the GATK this is not supported - we're actively working on this and will be available in the next weeks - unfortunately I can't give you an ETA yet.
In the mean time you can either use HC without ReducedReads or UG with ReducedReads
Mark A. DePristo, Ph.D.
Co-Director, Medical and Population Genetics
Broad Institute of MIT and Harvard