Figuring out which genes a set of SNPs overlap with

Question

[devenvyas]

I have a set of 1800 SNPs spread across all 22 autosomes. The data is in Plink format. I want to figure out which genes overlap each SNP, and whether they overlap coding or non-coding regions.

I was wondering what would be a good way to do this?

Answer 1

[WouterDeCoster]

The most straightforward would probably be to first convert your ped file to a vcf file and then use a variant annotator like annovar/snpeff/VEP on that vcf file.

[devenvyas]

For someone relatively new to this stuff, which one of those three do you think would be easiest to use? All three of them are already installed on my institutions computer cluster, so I just need to figure out which one to use.

[WouterDeCoster]

I think all should be fairly easy to use. Without good reasons I would first try VEP, if not happy with that move to spneff and then annovar. All should be fine.