I want to add VCFFilter 0.0.3 in Galaxy Tools, how do I do that...Please help.
Currently the version installed is 1.0.0 and this is giving error when I want to filter a vcf file to filter out the false positive sites.
I am trying to identify DNA polymorphic sites
Hello,
The older version of the tool is available in the ToolShed https://usegalaxy.org for installation in your own Galaxy. You must be an administrator to do this.
However, I wouldn't recommend that -- that tool version had some bugs, which is why only version 1.0.0_rc1+galaxy1 (the most current) is available at Galaxy Main https://usegalaxy.org. This version is what should also be what is used in a local or at any Galaxy server.
Galaxy itself and the related tools (including Freebayes) should also be installed to be current.
You can request a tool update if using some other public Galaxy server and the tool (or tools and potentially the server version) is not current. Contact the administrators directly as each public Galaxy is independently hosted.
Thanks & I'll reply to your other question, Jen, Galaxy team
Thanks Jennifer. I was able to run the latest version by giving filter criteria QUAL > 40
Related post: VCFFilter 1.0.0 fatal error with FreeBayes VCF input https://biostar.usegalaxy.org/p/28212/