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  • Trouble with making indel calls using UnifiedGenotyper

    I'm working with 100bp Illumina Paired end, and I have been following the GATK best practices v3.

    First, I mapped with BWA.
    In INDEL mode, UnifiedGenotyper returns nothing.
    Second, stampy.
    In INDEL mode, only one large indel, and it was a false positive.

    When doing base recalibration I did not have a list of known sites. Could this be such a significant problem that UG would return nothing?

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