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GATK for Nanopore data

Paola_OrsiniPaola_Orsini University of BariMember

I'm trying to use GATK to perform variant calling analysis with Minion Nanopore data. In details, I would like to ask you if someone has already used GATK to analyse Nanopore sequencing data, and if data processing analysis with GATK can improve homopolymer errors.
Thank you,

Paola Orsini


Issue · Github
by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, sorry for the late response. We don't have any experience with Nanopore data (haven't had any in our hands so far) so we can't advise you on this. If this data type suffers from lots of homopolymer errors, GATK will struggle in those areas, because that's already a bit of a weak spot. We have some development work underway to improve calls in regions with STRs but I don't know how much it will help with this datatype, and it will be a few months probably before those improvements make it into the GATK release.

  • lakhujanivijaylakhujanivijay IndiaMember

    Is there any updates on this one? Has GATK already implemented something for nanopore?

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    You may want to check responses from PacBio experiences since they act similarly except the nanopore has even longer reads. There should be some in the forum already.

  • manolismanolis Member ✭✭

    Is there any updates on this one? Has GATK already implemented something for nanopore?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @manolis

    We have not implemented nanopore yet.

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