Annotating alternate alleles of a SNP

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Annotating alternate alleles of a SNP

Mara Kim-2
Hello gmod-ers,

I was wondering what others have done to store supporting data for SNPs.  SNPs present an interesting challenge, as there are data pertaining to the site (Tajima's D, Fst, etc.) as well as data pertaining to different alleles at the site (eg. allele frequencies for different populations, selection coefficients, etc.).

The best practices on the wiki suggest using a single feature to denote the SNP itself, with alternate alleles as different ranks in featureloc using residue_info to describe the alternate sequences.  My question is, how have people been adding things like allele frequencies?

The lack of an analysisfeatureloc or featurelocprop tables make it difficult to be clear which variant is being referenced by a given annotation.  Does anyone have suggestions?

--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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