Mixing Snp From Different Hapmap Releases

Question

[Radhouane Aniba]

I am trying to extend a SNP list using a proxy search by LD blocks by SNAP but when I read the documentation I found that SNPs existing in HapMap release 2 differ and is not an extension of those existing in release 2

What is then the best way to mix SNPs from different HapMap releases ?

I downloaded the snps in Bed format and I am going to see if galaxy allow to do it, if someone have another idea please let me know

Cheers

Rad

Answer 1

[ff.cc.cc]

Imputation tools like Impute2 and mach use very dense panel of SNPs as reference data.

Maybe you can try here: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download_reference_data

They claim to have processed 1,000 Genomes files and HapMap 3 files so that they can be used as a single, composite reference panel with IMPUTE2.

Answer 2

[Larry_Parnell]

We use SNAP and set it to 1000 Genomes data for CEU (as most of the populations we study are of European origin). This seems to pose very few problems in terms of the proxy list. So, instead of extending to another version of HapMap, try extending to 1000G.

[Larry_Parnell]

Yes, imputation as mentioned by ffcccc is also good to add to the mix (+1).