Using dbSNP dataset

Question

[rotemkat]

Hi! I have a list of mutations and I want to check how many of them are germline mutations and appear in the dbSNP. I download the VCF file from dbSNP, but this is a very heavy file and i can't find a way to upload it and compare it with my list. Do you have any ideas for a solution for what i need?

I tried to download and install bcftools but for some reason can't use it (get multiple errors) and I'm not even sure this is the right direction for me.

Thanks in advance!

[Amitm]

Hi, You probably don't need to download dbSNP file yourself. Use a variant annotation program like VEP. On installing it locally you get annotation files which will have dbSNP (and 1000genomes etc.) variant allele frequencies incorporated. You could use the web interface of VEP as well (website down at moment but should be up soon).

There are other variant annotation tools like SNPeff which again have their pre-built anno. databases that are much easier to use than using dbSNP downloaded VCF yourself.

[Pierre Lindenbaum]

I tried to download and install bcftools but for some reason can't use it

first. fix this. And, in fact, this should be your question.