how to select candidate genes after resequencing

Question

[jane.zh]

Hi, I am now doing some researches of resequencing. Now I've got a large amount of SNPs, and want to utilize them to identify candidate genes. But I am very confused of it. How can I select these candidate genes? With the help of Ensemble or David, or any other tools?

[Ashutosh Pandey]

You need to elaborate your question or make it more clear. I quiet didn't get what you want to do?

[jane.zh]

I want to find positive select sweep, and locate some genes which participate in this positive selection. I've konown positons of SNPs, and I want to find those important genes through the information of these SNPs.

[Matthieu Miossec]

This paper might give you some helpful pointers:

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

[jane.zh]

Thank you very much!

Answer 1

[Emily]

The Variant Effect Predictor will tell you what genes your variants hit and what effect they have on them.

[jane.zh]

Thanks a lot!

Answer 2

[Maxime Lamontagne]

You could verify if your SNPs have potential deleteriousness effect with CADD (Combined Annotation Dependent Depletion) and choose the genes with the most probable deleterious SNPs.