Question: Haplotypes from SNP data
0
gravatar for admamajdi
12 months ago by
admamajdi0
admamajdi0 wrote:

Hello,

I want to generate haplotypes from SNP data such that for example I could use 4 SNPs to create a haplotype and so on.

Any idea how to get this done and if there is any software that it can be used for this?

Thanks!

snp genome • 425 views
ADD COMMENTlink modified 12 months ago by Charles Warden7.5k • written 12 months ago by admamajdi0
0
gravatar for Charles Warden
12 months ago by
Charles Warden7.5k
Duarte, CA
Charles Warden7.5k wrote:

I've done some testing with HLA haplotypes, and phasing is supposed to help with defining SNP chip data.

I am not sure about what publication to currently list, but I think a sufficient number of SNPs probably can give reasonable haplotype assignments (at least when haplotypes are sufficiently different, and quality of the assemblies are relatively clear - or at least well characterized in independent studies).

So, my guess is that you may probably want to have more than 4 SNPs, but I think the specifics will vary from project to project.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Charles Warden7.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1776 users visited in the last hour