Problem filtering by insert size using Bamtools

Dear all,

I attempted to filter a BAM file using Bamtools to select for reads with insert size < 150bp. However the insert size distribution of the post-selection BAM file indicate somewhat a partial selection.



Can anyone advise on how to troubleshoot this?



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Very odd. What tool version and parameters were used?

I suspect there is a problem in the filter term used. It should be formatted like this (no spaces, no quotes): <=150

Try that and if it doesn’t resolve the problem, click on the job details icon:


Then post the “Job Information” (first line that reports Galaxy Tool ID: is enough) and the " Tool Parameters" (all) portions back and we can try to help sort out what is going on. Screenshot(s) or copy/paste as quoted text to preserve formatting.

If you know the public Galaxy server URL or the version of Galaxy you are running yourself, that might also help.


Tried <=150 with same result obtained.

And this is the information I got.

On the site it says - Galaxy version 18.09

Galaxy Tool ID:

Tool Parameters

Input Parameter Value Note for rerun
BAM dataset(s) to filter 90: AL0035-original
Select BAM property to filter on insertSize
Filter on insert size <=150
Would you like to set rules? false

Inheritance Chain

Filter on data 90: Filtered BAM

Job Dependencies

Dependency Dependency Type Version
bamtools conda 2.4.0

Dataset peek

Binary bam alignments file

Thanks again for helping.

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I was unable to reproduce a filter result like yours at (same tool version, test dataset).

To further troubleshoot, please either send me a direct message (here) that includes your registered account email at Galaxy Main ( or send an email from your registered account email address to the private mailing list that includes a link to this post. Either way, please leave the datasets involved undeleted so we can review as an admin and try to figure out what may be going wrong.


My login email is <redacted from public site>.



Thanks, got it and removed it from the public post. More feedback after review.

Next time you can direct message with private information – go into your message and ask “discobot” to learn how.