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

aiglos

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

Geraldine_VdAuwera

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.

aiglos

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_VdAuwera

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

aiglos

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_VdAuwera

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.

aiglos

Geraldine, thanks a lot for your responde!

aiglos

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

aiglos

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_VdAuwera

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.

aiglos

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!)