Question: tool to translate/convert locus among species ?
0
gravatar for houkto
5.2 years ago by
houkto60
UK
houkto60 wrote:

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

snp convert loci translate species • 1.2k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by houkto60

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.

ADD REPLYlink written 5.2 years ago by houkto60

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 ?

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Ashutosh Pandey11k

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

ADD REPLYlink written 5.2 years ago by houkto60
2
gravatar for Devon Ryan
5.2 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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.

ADD COMMENTlink written 5.2 years ago by Devon Ryan90k
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