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HaplotypeCaller and Reduced BAMs

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


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.



  • delangeldelangel Dev Posts: 71

    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.

  • Mark_DePristoMark_DePristo Administrator, Dev Posts: 153 admin

    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

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