varscan output

[jgSoton]

Hi,

Does anyone use varscan?

I get this message "Not resetting normal file because chr10 < chr9". (repeated many times)

Any idea what it means or if its a problem?

Thanks,
Jane

[dkoboldt]

Jane,

This is just a warning printed by VarScan as it's simultaneously parsing normal and tumor files. As long as your output files contain all of the chromosomes that you expect, you can safely ignore it. If you encounter further problems, please shoot me an e-mail to dkoboldt (at) genome (dot) wustl (dot) edu.