SNP and Haplotype differentiation

Question

[pakeeza]

Hi,

I am naive in using SNP and Haplotypes. I have SwissProt Variants and I want to know which of these Variants are in Haplotype. Can anybody guide me how to determine it? Is there any tool available?

[LauferVA]

please tell us more about what type of data you have in hand.

Answer 1

[pakeeza]

So I have only variants from UniProt natural Variants data and I want to know whether my SNPs act as haplotype or not.

Answer 2

[LauferVA]

Part of the problem in helping you is there are SO MANY tools available. Are you interested in one specific ethnicity, or all ethnicities? Linkage changes between ethnicities, sometimes very little, sometimes greatly.

There are many approaches you could take. You could download Hapmap data, then calculate pairwise linkage disequilibrium using something like PLINK. http://pngu.mgh.harvard.edu/~purcell/plink/

Or if you want to muck around with some whole genome data, you could download data from the 1000 genomes project then use vcftools --hap-r2

You could also use a tool specifically designed to analyze linkage such as phase such as SNAP.

https://www.broadinstitute.org/mpg/snap/doc.php

You can also get a lot out of HAPLOVIEW if you dig around with it. https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

I remember seeing a database of linked variants before that has pre-calculated values for different haploblocks, but it has been long enough that I cannot re-locate it.. if you want to find such a list without generating it from data you download you CAN find things like this, unfortunately I have forgotten where I found this.

Does this help?

Answer 3

[pakeeza]

I wonder all these deal with dbSNP ID but I have several variants which do not have dbSNP ID. There is one way to look at it using UCSC gene browser and looking in Common Gene Haplotype Alleles But I still want some other source because that data is not downloadable and become tedious to lookup for all genes when data set comprise of several hundred genes.

[LauferVA]

If this is the case, then calculate linkage directly using the 1000 genomes data.