whole exome variant filtering

Question

[storm1907]

Hello, I need to do whole exome variant analysis from ready vcf.gz files. Only option I know is filtering through Illumina Variant Interpreter

Are there better options for whole exome variant filtering than Variant Interpreter?

Thank you!

[Hamid Ghaedi]

Maybe duplicate of this thread: C: Variant filtration software

You can find a list of tools there.

[Kevin Blighe]

Well, in which way do you want to filter? - low read depth?; strand bias?; functionality / pathogenicity [of the variants]?

For ease of use, Ensembl's Variant Effect Predictor may be what you need.

[Kevin Blighe]

Thanks Hamid