tool to translate/convert locus among species ?
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7.5 years ago
houkto ▴ 80

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

loci species SNP convert translate • 1.6k views
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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.

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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 ?

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

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7.5 years ago

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.

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