2.9 years ago by
What output setting for Mpileup are you using? The default should work with the filter. Other options will not due to format incompatibilities. The data examples on each tool form has examples for comparison.
We can troubleshoot more if you are still not sure of the settings and the output each produce versus your data. Send in a bug report from the error dataset (via green bug icon). Please make certain that all input and error datasets are undeleted.
(This assumes you are working at http://usegalaxy.org. If not, maybe see if you can reproduce there- that can be useful information if we need to expand the troubleshooting for a local or cloud).
Thanks, Jen, Galaxy team