I have a large list of chromosomal regions for which I would like to generate +/-10 bp of flanking sequence surrounding all SNPs for all alleles that are found in these regions. A hypothetical output for two alleles found in a given range on chromosome 1 might look like this:
>chr1|1234500|G AAAAAAAAAAGAAAAAAAAAA >chr1|1234500|C AAAAAAAAAACAAAAAAAAAA
Normally, I generate an XML query and download the data from BioMart. Using BioMart my query always hangs (Biomart seems unusually slow lately). Does anyone know how I can generate the sequences for all alleles of all SNPs found within a given range using something other than BioMart? Thanks in advance for any help you can provide.
I should also mention, that another solution that would work perfectly fine would be a method to download all the DB132 SNPs with flanking sequences. From there I can whip up a script to filter only the sequences I need from my regions of interest.