Best practice for variant calling on Ion Torrent data with GATK

zhangxzhangx Posts: 4Member
edited October 2012 in Ask the GATK team


I wonder how well GATK works with Ion Torrent data. Is there any recommended practice to handle Ion Torrent data, especially SNP and indel calling, with GATK?

Thanks, XZ

Post edited by Geraldine_VdAuwera on

Best Answer

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Developer admin
    Answer ✓

    This is a very good question. We do have reasonably extensive experience with GATK on Ion Torrent (PGM and Proton) and we've been meaning to put together a best practices doc for Ion Torrent. My two cents: we can do reasonably well for SNP but indels are I think impossible today given the homopolymer error mode of that sequencers. I have yet to see any compelling evidence that indels can be done effectively using any approach -- not just GATK -- including the example results on the Ion Community itself.

    -- Mark A. DePristo, Ph.D. Co-Director, Medical and Population Genetics Broad Institute of MIT and Harvard


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