What is the best annotation tool?

Question

[Sonia]

Hi all,

I want to annotate ~200 VCF files for cancer patients. my question is that what's the best tool for annotating these bulk files? Do you recommend using multiple tools and merge the results?

Thanks for any help

[Nitin Narwade]

What sort of annotations you are looking for??

[Sonia]

Dear Nitin, I'm not sure if I correctly understood what you mean, but I want to use the stand-alone tools and need to annotate the somatic mutations by them.

[ponganta]

What kind of data do you have?

[Sonia]

Dear ponganta,

I have the VCF files of the WGS and want to annotate them.

Answer 1

[Kevin Blighe]

Over the years, the ones that I have used most are:

• Variant Effect Predictor (VEP)
• ANNOVAR

Both require some concentrated setup time, but, once done, they'll be your friends for life.

Kevin

Answer 2

[colindaven]

• VEP is very nice.
• SNPeff is popular.

More info here:

updated clinical variant annotation software and databases