Getting Conservation Scores For Specific Sites

Question

[Rubal7]

Hello everyone,

I have a VCF file containing changes in a population of Rattus norvegicus. I would like to rank these changes by the conservation scores of the effected sites. I know that there are various conservation tracks available, they often seem to be mapped to the human genome. Does anyone know a nice way to retrieve conservation scores for thousands of sites in a non-human genome? I see that some browsers let you view a track but it's not clear to me how to submit sites and get a list of conservation scores. It looks like the most powerful dataset for identifying conserved sites is the 29-mammalian genomes set from the Broad, but I'd be happy to start with other datasets if its simpler to get this information.

Any help or suggestions are greatly appreciated. Also if anyone has any related tips or thoughts on conservation scores I'd be interested to hear them. They seem like a very powerful way to predict functional variants in parallel with methods that look for non-synon changes/stop codons etc like the variant effect predictor. Thank you in advance!

Cheers, Rubal

Answer 1

[JC]

the conservation scores for rat are in http://hgdownload.cse.ucsc.edu/goldenPath/rn4/phastCons9way/ but it only compares with 8 species. The human-centric conservation scores is more complete (44 species: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/). I think you can use LiftOver to map your regions in this path: rat coords -> hg18 coords -> conservation in 44 species.

[Rubal7]

Thanks very much for your help, I'll look at both of these.