Rare Variants From Annotated Vcf File

Question

[Ron]

Hi,

I have annotated my vcf file of 20 samples from Unified genotyper using the following steps.

Unified genotyper->Variantrecalibration->Applyrecalibration->VariantAnnotator

My question is how should I proceed if I have to select rare variants (MAF<1%) for the candidate genes that I have,for each of these 20 samples?

[Zev.Kronenberg]

Are you are looking for disease associated variants in a cases/controls study? Our lab wrote a tool that may work for you: http://www.yandell-lab.org/software/vaast.html ...

Answer 1

[Charles Warden]

You can use 1000 genome and/or ESP frequencies to determine rare variants.

There are lots of tools to accomplish this, with ANNOVAR being one of the most popular:

http://www.openbioinformatics.org/annovar/

This software also has a web interface, called wANNOVAR:

http://wannovar.usc.edu/

SeattleSNP can also accomplish this:

http://snp.gs.washington.edu/SeattleSeqAnnotation138/

It is possible that you may need to reformat some files in order to get the variant annotation to work properly.