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  • Papers Describing Indel Calling Algorithms

    Does anyone happen to know where I could find detailed information on the algorithms used to call indels and assign confidence for the following programs:

    * GATK
    * SAMTOOLS
    * Vardict
    * FreeBayes

    I gather some of the publications out there are out of date.

  • #2
    If you are interested in the algorithms behind indel calling in general, the method used by RTG Core for indel calling (and complex haplotype calling) is described in: http://www.ncbi.nlm.nih.gov/pubmed/24874280
    Len Trigg, Ph.D.
    Real Time Genomics
    www.realtimegenomics.com

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