Finding SNPs that have been pre-defined

[Magpie101]

Hi All,

This is a bit of a beginners question but here goes....

I have a dataset of Illumina paired-end reads mapped to a reference genome. I want to use genome locations of existing SNP's in an input file to find them in my dataset. I've used Bedtools before to find unique SNPs but I'm not sure how to ask it to use an input file with a-priori defined SNPs and output these calls (or even whether bedtools is the best tool for this job). I'd also like to set a min and max read depth if possible.

If anyone has the expertise to point me in the right direction I'd be ever so grateful.

Cheers
MP

[Jessica_L]

bedtools would work for that. Check out the intersect command-- you can use a bed or a vcf for locating variants in your dataset. There are several other options, too-- vcfintersect from the vcflib toolkit, etc.