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Varscan2 filters AND usability of the tool - looking for opinions
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20 months ago
user230613 • 280
Europe

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:

Do you have any experience using VarScan2 tool?

Thank you

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