Question: Genotype Concordance - bcftools - stats?
gravatar for m28happ95
27 days ago by
University of Nebraska - Lincoln
m28happ9510 wrote:

I've been trying to find a tool in galaxy that works for calculating genotype concordance between vcf files. Recently I came across bcftools - stats, which seems to have what I need. However, when I try to run it I get an error saying " bgzip: command not found ". I've checked the tool installation and there are no missing dependencies. I'm running this on a local instance I installed a couple weeks ago.

Any thoughts? I'm pretty new to this, so let me know if I can provide any more info to help solve this issue.

ADD COMMENTlink modified 25 days ago by Jennifer Hillman Jackson23k • written 27 days ago by m28happ9510

Hi -

Are you using a local Galaxy version 17.09 installed using git? Or did you use another method/source? If the below doesn't work, let us know since this info will help when testing.

As a quick way to potentially resolve this - have you installed samtools yet? If not, try doing that to see if the dependency problem resolves. We can follow up from there, to troubleshoot more and potentially report a problem with the repository to the tool authors.

Thanks! Jen, Galaxy team

ADD REPLYlink written 27 days ago by Jennifer Hillman Jackson23k
gravatar for Jennifer Hillman Jackson
25 days ago by
United States
Jennifer Hillman Jackson23k wrote:


Update: I asked the IUC developers (at their gitter channel) if there were any known issues and was informed that a conda bug is impacting some tool installs ( The devs are working to correct this. I couldn't determine, for Galaxy tool installs, and specifically bcftools, if this means that directly installing the correct version of the conda dependency(ies) is a potential solution or not. I asked for feedback and will post back here once there is a confirmed workaround (if any).

Meanwhile, you could also review the conda ticket and if you want and/or see if installing the dependencies directly with conda solves the problem. Under the Admin tab, section Tool Management > Manage dependencies, do a "find" with your web browser will locate those associated with bcftools. I suspect you will find that some are not installed or were installed but with an incompatible version (if I understood that part of the conda ticket correctly!).

This could be a bit tedious to do (install, set paths, etc) - so the best workaround, for now, is probably to instead install a version of bcftools stats that did not use conda dependencies. That would be the wrapper version 1.3 from Jan 2017. It is here in Main Tool Shed and you can also navigate to this earlier version during admin install: (note: the tabix warning on the repo can be ignored). Or if you are installing the entire bcftools suite, use the same version from Jan 2017.

You should probably uninstall the current version of bcftools first so that it is clear in the tool panel which tools are usable without having to click on them to review the version. Or you could create/name a new tool group, in an informative way, to place the earlier version into during install (full suite or just this tool).

This tool is not installed at Galaxy Main (, but it is at Galaxy Test ( This is also the earlier version 1.3. Not all of the dependencies are installed, so using the stats tool there might be problematic, but you could try just to see how the tool works. We really do testing on that server and configuration can change at any time, so it is not recommended to do analysis there beyond trying out tools/tool versions not on Main (to see how they work - when working!) or when getting involved in new tool testing.

Hope that one of these choices will work out for you! Jen, Galaxy team

ADD COMMENTlink written 25 days ago by Jennifer Hillman Jackson23k

Hi Jen -

Yes, I am using local galaxy version 17.09, installed using git. I have installed samtools 1.2 - which didn't resolve the issue. I also backed up to the January 2017 version of bcftools_stats, after uninstalling the latest version, which resulted in the same error:

Fatal error: Exit code 127 () /home/mhapp95/galaxy/database/jobs_directory/000/584/ line 9: bgzip: command not found

I looked under "manage tool dependencies" after that, and I think it might be some issue with HTSlib? In both the recent and January installations of bcftools I tried, over to the right of the row for the HTSlib requirement was a red "x" that I could hover over and a text box would appear saying "dependency not resolved"

Thanks for looking in to this.

ADD REPLYlink written 22 days ago by m28happ9510
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