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Best practice for variant calling on Ion Torrent data with GATK

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

Hi,

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 Broad InstituteMember Posts: 153 admin
    Accepted 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

Answers

  • Mark_DePristoMark_DePristo Broad InstituteMember Posts: 153 admin
    Accepted 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

  • zhangxzhangx Member Posts: 4

    Thanks for your prompt response, Mark. I understand that the variant caller developed by Ion Torrent uses a modified version of GATK, which includes a flow space modelling function to tackle the homopolymer issue. Do you have any experience with that? If I want to call INDELs with on Ion data with GATK now, would you recommend using the current INDEL pipeline -- indel realignment, UnifiedGenytyper with glm set to DINDEL and hard filtering?

  • Mark_DePristoMark_DePristo Broad InstituteMember Posts: 153 admin

    All good questions -- things we'll address on the best practices entry.

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

  • NielsNiels Member Posts: 2

    Is there more known about using GATK for variant calling SNPS and Indels?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,414 admin

    Niels, if you mean to ask about calling variants on Ion Torrent data, we have not yet had the time to produce that documentation.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,414 admin

    Update to this thread: we are no longer working with Ion Torrent at all and will not produce best practices for dealing with this data type.

    Geraldine Van der Auwera, PhD

  • SyedSyed IndiaMember Posts: 11

    So no way we can use Ion Torrent data with GATK for variant calling ?
    Thanks
    Najeeb

  • SheilaSheila Broad InstituteMember, Broadie, Moderator, Dev Posts: 4,590 admin

    @Syed
    Hi Najeeb,

    Sure, you can use it on your own, but we won't be able to help you if you have issues.

    -Sheila

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