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 about half of them are potentially novel SNPs in the population I’m studying, how can I quickly and automatically fetch flanking sequence from the reference sequence? I asked how to do this on previously mentioned Biostar, and got several answers within minutes.
Fortunately this can easily be done using R and Bioconductor. For several reasons BioMart wouldn’t do what I needed it to do, and I don’t know the UCSC/Ensembl schemas well enough to use a query or the Perl API.
This R code below (modified from Adrian’s answer on BioStar) does the trick: