Retrieve Sequence Near Snp

Question

[omicj]

Hi all

I try to retrieve the sequence near SNP I found from sequencing data. Is there any efficient way to do that?

Thanks
Jay

[Alex Paciorkowski]

What organism? How much sequence around/near your SNP? What do you want to do with it after you have it?

Answer 1

[Devon Ryan]

If you have a copy of the genome (I'm assuming that this is your own sequencing data, in which case you likely would), just use "samtools faidx chromosome:region.start-region.end".