Are there any tools to map SNP/SNV consequences against a reference genome for sequencing data of different strains or close species? For example, for mouse strains or subspecies against the consensus BL6, or for Drosophila strains and subspecies against the Drosophila melanogaster reference.
The SeqAnt (Sequence Annotater) service from a group at Emory maps SNP/SNV consequences to the reference human, mouse, fly, or worm genomes, or lets you supply your own reference genome. This might be what you're looking for.
Description of the annotation from their website:
"Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser."
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