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Identification of all SNPs in a haplotype based on a single SNP

aiglosaiglos Posts: 6Member

Dear all!

Is it possible to identify all SNPs in a haplotype using a single SNP?

For example, input file: list of SNPs. Output file: list of all SNPs correlated with each SNP in the input file.

Thanks in advance!

Sincerely,
aiglos

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,532Administrator, GATK Developer admin

    Hi Aiglos,

    It sounds like what you want to do is simply phasing. We do have tools to do that, if that's what you want.

    Geraldine Van der Auwera, PhD

  • aiglosaiglos Posts: 6Member

    Hi Geraldine!

    Thanks a lot for your answer!

    Would you be so kind to be more precise?

    Do you mean HaplotypeCaller or something else?

    Thanks in advance!)

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,532Administrator, GATK Developer admin

    I mean genotype phasing and refinement, as discussed in the presentation you can find here (toward the bottom of the page):

    http://www.broadinstitute.org/gatk/guide/events?id=2038

    Geraldine Van der Auwera, PhD

  • aiglosaiglos Posts: 6Member

    Geraldine,
    thanks a lot for the video!

    I'm working on identification of correlated SNPs in (somehow) predefined haplotypes for European population based on a single SNP.
    So, I have a list of SNPs and want to receive all SNPs in a haplotype(s) for each SNP from original list.

    Sorry for ambiguity)

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,532Administrator, GATK Developer admin

    Ah, I see... we don't have anything specific to do that, sorry. Depending on what data format your haplotypes are in, you can probably get this done with a fairly simple script.

    Geraldine Van der Auwera, PhD

  • aiglosaiglos Posts: 6Member

    Geraldine, thanks a lot for your responde!

  • aiglosaiglos Posts: 6Member

    To tell your the truth, I don't have calculated haplotypes, hope to find them already in Gatk)

  • aiglosaiglos Posts: 6Member

    Dear Geraldine!

    I've received another task. Is it possible to obtain haplotype blocks for Prodynorphin (PDYN) gene for European population?

    In other words, I'd like to have different phasing SNPs blocks specific for, let say, 95% of European sample.

    Maybe I'm not clearly explain the assignment, I'm very new in the field, sorry)

    Thanks in advance!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,532Administrator, GATK Developer admin

    No, this is not something you can do simply with the GATK. You can phase samples with GATK, but then you'll need to do a significant amount of additional data manipulation, either with custom scripts or with other software packages.

    Geraldine Van der Auwera, PhD

  • aiglosaiglos Posts: 6Member

    Dear Geraldine!

    Thank you so much for the quick answer!

    Hope, I'll be happy with Plink proxy association test:
    http://pngu.mgh.harvard.edu/~purcell/plink/proxy.shtml

    Have a nice day!)

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