OMIA: get all dog SNP locations and then download fasta surrounding SNP

Question

[rachel]

I suspect this is a really stupid question.

I'd like to download all the known dog SNPs/indels in OMIA and around 100bp genomic sequence on either side of the SNP/indel. Is there an easier method of doing this than manually extracting the SNP genomic locations and accession and then automating the slicing of those locations? I'm happy to code it up in python but surely there's an easier way to access all the dog disease-causing SNPs ?

[finswimmer]

Hello rachel,

I couldn't find out which data format the informations about the SNP are. Could you please post an example?

If one have the position of the SNPs, we can create a bed file out of this and use bedtools getfasta to fetch the corresponding sequence out of the reference genome.

fin swimmer

[rachel]

I think you've re-iterated my question. I need to automate getting the SNP positions out of OMIA. Once I have the SNP positions, getting the 100bp each side is easy.

Here's a link to one of the pages on OMIA where there is specific SNP information http://omia.org/OMIA000187/9615/ There just doesn't seem to be a way to automate getting the specific SNP locations out of OMIA for an organism (in this case, dog) ?

[finswimmer]

Oh sorry, misread your first post. I thought you've already downloaded the SNP data. I couldn't found either a simple way. Sorry.

fin swimmer