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

Member Posts: 6

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.

Sincerely,
aiglos

Tagged:

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

• Member Posts: 6

Hi Geraldine!

Would you be so kind to be more precise?

Do you mean HaplotypeCaller or something else?

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

Geraldine Van der Auwera, PhD

• Member Posts: 6

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)

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

• Member Posts: 6

Geraldine, thanks a lot for your responde!

• Member Posts: 6

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

• Member Posts: 6

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)

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

• Member Posts: 6

Dear Geraldine!

Thank you so much for the quick answer!

Hope, I'll be happy with Plink proxy association test: