tool to translate/convert locus among species ?

Question

[houkto]

Hi all,

Is there an existing tool or way to convert / translate a loci such as SNP (e.g GWAS SNPs) from human to another species like mice, rat ?

What I am trying to achieve is translate GWAS SNPs of a phenotype from a human study then to lookup the location of the SNP in mice (with the same phenotype ). Is this possible ?

Thanks

[houkto]

Thanks for you answer, I used it before leftover used between assembiles of the same animal not between species. It was the first thing I did but it I get a failed message when ever I tried to convert a snp which makes me think its not working.

[Ashutosh Pandey]

The conversion may or may not work for a SNP depending on if the two species share the region harboring the SNP. But most of the markers should be shared between mouse and human. Can you give an example ?

[houkto]

Thats very true, I just did 72 SNPs query and came up with sucessful conversion. :D thanks everyone.

Answer 1

[Devon Ryan]

The online liftOver tool would be my first thought. You can also download the command-line version if it makes life easier. Either way, just convert the SNP positions to BED format and usage should be straight forward.