mapping snps to fucntional class and genes

Question

[Gbn]

Hi,

I have mapped a set of SNPs (rs#) using biomart within R to consequence types, but there are cases where each SNP is mapped to multiple functional class types with identical chromosome and position. How do I resolve the ambiguity and select the correct functional class.

Thanks

Answer 1

[kautilya]

Usually this is the case where a single SNP has multiple effects. For example a SNP could have a non-synonymous effect on one gene while being downstream of another. One thing you can do in such a scenario is shortlist the most damaging effect. If you use a different tool base then snpEFF+GATK VariantAnnotator can do this for you.