Minor allele frequency and damaging prediction

Question

[cristinam09]

Hello

I am analyzing variant calls of tumor samples versus the reference hg19 human genome. Which are the best tools to determine the MAF possibly divided by ethnicity and to predict the damaging potential of the variant?

Thank you for helping

Answer 1

[Maxime Lamontagne]

To predict the damaging potential of the variant:

• CADD
• ClinVar
• Ensembl Variant Effect Predictor

And so many more. Read the article of CADD (A general framework for estimating the relative pathogenicity of human genetic variants) to have a good list of software and websites.

To determine the MAF possibly divided by ethnicity: I don't understand what you want.

Answer 2

[NB]

There are many tools out there if you look around, for example: http://evs.gs.washington.edu/EVS/, https://bioq.saclab.net/, http://hapmap.ncbi.nlm.nih.gov/downloads/frequencies/?N=D etc., you can download the database and write a script to query the Rs ids of interest. Then, there is annovar as well, which implements the prediction tools.