Question: VCFFilter tool update from version 1.0.0 to 0.0.3
0
gravatar for premraj.preeti
6 months ago by
premraj.preeti10 wrote:

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

ADD COMMENTlink modified 6 months ago • written 6 months ago by premraj.preeti10

Related post: VCFFilter 1.0.0 fatal error with FreeBayes VCF input https://biostar.usegalaxy.org/p/28212/

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

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

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
0
gravatar for premraj.preeti
6 months ago by
premraj.preeti10 wrote:

Thanks Jennifer. I was able to run the latest version by giving filter criteria QUAL > 40

ADD COMMENTlink written 6 months ago by premraj.preeti10
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