Variant annotation using Illumina Basespace Variant Interpreter

Question

[smrutimayipanda]

Hello, I am working on whole exome data (Illumina data) and now I want to do variant annotation. I used several methods for annotation but not getting enough information. I heard about Illumina Basespace variant Interpreter, but I dont know how to use it. If anyone has an exposure, please help me in this. Thank you.

Answer 1

[Zuber]

You can analyse/interpret/annotate it using Nirvana through command line. Only drawback is json (output) file filtering. (https://illumina.github.io/NirvanaDocumentation/)

please let me know if anyone or you can find a tool to easily filter the data.

[bharata1803]

Nirvana has Jasix to filter that works similar with tabix.