Get location annotation information from SNP position in genome

Question

[matt.christmas85]

Hi,

I have a list of ~60,000 SNPs identified by chromosome number and position for Eucalyptus. I am looking for a quick way to get information on specifically where these SNPs sit within the genome, e.g. are they within introns, coding regions, UTRs, etc? Is there a tool out there that can take genome position information as input and generate annotated details of where these SNPs lie and, therefore, their potential functional importance?

[Jeffin Rockey]

a) Please see whether SnpEff tool can meet your requirement.

b) Alternatively if you have a gtf/gff3 , using bedtools intersect with appropriate options should also help.

[matt.christmas85]

Thanks Jeffin, SnpEff was exactly what I was after. I just formatted my SNP locations into vcf and SnpEFF did the rest!

Cheers,

Matt

[Jeffin Rockey]

Matt,

Very glad to know that it helped.

Jf