Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

April 12, 2011

(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)

I’m working on a project using next-gen sequencing to fine-map a genetic association in a gene region. Now that I’ve sequenced the region in a small sample, I’m picking SNPs to genotype in a larger sample. When designing the genotyping assay the lab will need flanking sequence.

This is easy to get for SNPs in dbSNP, but what about novel SNPs? Specifically, given a list of genomic positions where

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