Question: mapping snps to fucntional class and genes
0
gravatar for Gbn
4.5 years ago by
Gbn0
Gbn0 wrote:

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

snp R gene • 1.2k views
ADD COMMENTlink modified 4.5 years ago by kautilya400 • written 4.5 years ago by Gbn0
0
gravatar for kautilya
4.5 years ago by
kautilya400
United States
kautilya400 wrote:

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.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by kautilya400
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