Annotate Variants with Pharmacogenomic Data

Question

[nilakshafreezon]

I have developed a pipeline for variant calling from exome sequence data, and I currently use ANNOVAR to annotate the obtained variants. But I would like to extend my analysis further with pharmacogenomic data as well. PharmGKB is a good source but it does not have any annotation facilities. Anybody know a good tool to do this or any alternative approach is highly appreciated. :)

Thanks in advance.

Answer 1

[Pavel Senin]

There is KEGG Medicus which has a set of genomic markers and drugs/interactions data. Their API is quite user-friendly.

[nilakshafreezon]

Thanks I'll look at it