For my variant analysis work flow, I tried using Varscan but the pileup data is not been able to be detected. Even after using the Mpileup format, the appropriate data is not visible or selected. Can anyone help me out.
Assign the pileup datatype to the input for the tool to accept it on the tool form. https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset
Note that Mpileup will produce either VCF or Pileup ouput. Make sure that it was run to produce pileup format to use it with Varscan.
If you are working someplace other than http://usegalaxy.org, and this does not solve the issue, the administrators of that instance should be contacted - there could be a problem.
Best, Jen, Galaxy team