Question: Filter Pileup Error in SAMtools
gravatar for john.doyle
2.9 years ago by
john.doyle0 wrote:


I am a new user to Galaxy and am having trouble with a filter pileup error. The error message I am receiving is as follows: "Coverage column 4 contains non-numeric values". I tried converting the Mpileup file to pileup format, but pileup filter still did not work. Any thoughts on where I am going wrong?



ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson25k • written 2.9 years ago by john.doyle0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello John,

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 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

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k
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