best way to get chimp-human homologous sites

Question

[abascalfederico]

Dear all,

I have my matrix of variant sites for different human individuals and need to incorporate chimp. I am aware of a couple of ways of doing this: 1) liftOver from human to chimp and get the chimp state (pairwise alignments) 2) read the "6 primates EPO" Ensembl alignments and extract the mappings human-chimp and the corresponding chimp states (multiple alignments)

But there are probably other ways. And I guess someone else must have done this before (that would safe me some work). Do you know where can I find the data or, if not, what would be the best way to do make it?

Many thanks, Federico

[GenoMax]

Using MafFilter may be an option.

[abascalfederico]

Many thanks Gabriel and genomax2, both very helpful!

Answer 1

[Gabriel R.]

The 2 ways you mentioned are the only ones I know about.

I have used the EPO alignments. You get the raw alignments from the ensembl ftp site. ftp://ftp.ensembl.org/pub/release-75/emf/ensembl-compara/epo_6_primate/

The format is not easy to parse and created a parser for it: https://github.com/grenaud/epoParser It parses the EPO data and provides columns for human/chimp/gorilla and their ancestor given that a region is uniquely defined across various species. Feel free to fork it and modify it as you wish.

Hope this helps a bit.