Varscan2 filters AND usability of the tool - looking for opinions

Question

[user230613]

Hi,

I'm going to perform a somatic variant calling using tumor/normal paired experiment and Varscan2 tool. Reading the documentation I have realised about this three filters available with the tool: fpfilter, somaticFilter and processSomatic. Anyone knows which one I should use to filter the somatic calls or any recommended workflow - best practices?

EDIT: I've been further investigating and now I'm wondering if VarScan2 is really supported and updated tool. I have read a loot of questions without answers across different repositories, like:

• Sourceforge
• GitHub

Do you have any experience using VarScan2 tool?

Thank you

[ATpoint]

How did it turn out for you?