How to annotate variants offline using ANNOVAR?

Question

[vinayjrao]

Hi,

I have been using wANNOVAR to annotate the variants I obtained, but I was informed that wANNOVAR is outdated, and it is better to download ANNOVAR and run it locally. If anyone has used ANNOVAR on their local systems, could you please tell me the Additional Databases I will have to download to get an output similar to the one generated by wANNOVAR (I know that the version has to be common across all).

Not all columns in the output are meaningful to our analysis, but I want to replicate it to compare one file analyzed by ANNOVAR and wANNOVAR to understand the differences between the two.

Any help in this regard will be deeply appreciated.

Thanks in advance.

Answer 1

[brunobsouzaa]

You can get all info here

[vinayjrao]

I had gone through that, but the sample output file provided contains fewer number of column as compared to the wANNOVAR output.

[brunobsouzaa]

Check which info you need on your annotated file, them download the annotations according to what is provided on annovar web page and include in the command line! Usually, the dbNSFP gives most of what you need!

[vinayjrao]

Sure. Will check and update. Thank you.