Question: Varscan2 filters AND usability of the tool - looking for opinions
gravatar for user230613
3.3 years ago by
user230613280 wrote:


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

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by user230613280

How did it turn out for you?

ADD REPLYlink written 2.8 years ago by ATpoint36k
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