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Best practice for variant calling on Ion Torrent data with GATK

zhangxzhangx Member
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
    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.

Answers

  • Mark_DePristoMark_DePristo Broad InstituteMember
    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.

  • 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

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

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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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.

  • SyedSyed IndiaMember

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

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @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

  • snijeshsnijesh hosurMember

    @Geraldine_VdAuwera @Sheila
    Is it difficult to make a pipeline for Ion torrent data. I don't feel good when I heard GATK does not give support for best call practice

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @snijesh
    Hi,

    I think the issue is that the sequencer has some funny indel error modes. GATK is not designed to handle those. But, you are free to use the Best Practices workflow and try. We just cannot guarantee the best results, especially around indels. If you do a search for Ion Torrent, you may find some helpful threads.

    -Sheila

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