Question: Figuring out which genes a set of SNPs overlap with
0
gravatar for devenvyas
3.6 years ago by
devenvyas620
Stony Brook
devenvyas620 wrote:

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?

snp gene • 789 views
ADD COMMENTlink modified 3.6 years ago by WouterDeCoster43k • written 3.6 years ago by devenvyas620
0
gravatar for WouterDeCoster
3.6 years ago by
Belgium
WouterDeCoster43k wrote:

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.

ADD COMMENTlink written 3.6 years ago by WouterDeCoster43k

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.

ADD REPLYlink written 3.6 years ago by devenvyas620

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.

ADD REPLYlink written 3.6 years ago by WouterDeCoster43k
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