Aidan Matzko

Dan, I have figured out the issue. mpileup2snp produces data which is formatted differently than somatic. Thus, is the filter only applicable to tumor normal data? Also, we are from the OSU CCC. Could you send me your email so I could contact you about having my team meet you to talk about VarScan? Thanks!

Note that we are using version 2.3.9. Has this been updated in a more recent version?

Hello, I'm trying to run the fpfilter on output from varscan somatic, however it appears the filter is setup to accept input from a tab seperated file, whereas the output from varscan somatic is both tab seperated and semicolon seperated. Am I missing something? Thanks! Aidan