Question: HOW TO COMBINE VARIANTS IN CLOUDMAP IN GALAXY
0
gravatar for supinderkr
13 days ago by
supinderkr0
supinderkr0 wrote:

Hi Trying to run this toolbut showing error dont know why please help and suggest its urgent

https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/variant_combine/gatk_variant_combine/0.0.4

tophat galaxy cloudmap • 33 views
ADD COMMENTlink modified 10 days ago by Jennifer Hillman Jackson22k • written 13 days ago by supinderkr0
0
gravatar for Jennifer Hillman Jackson
10 days ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

All GATK tools at http://usegalaxy.org have been deprecated and are no longer supported. I don't think that the authors of the newer version of GATK tools in the Tool Shed (for a local or cloud Galaxy) are supporting those anymore either, due to licensing and other complications.

Instead, we suggest using alternative methods/tools for variant analysis. - Please see the tutorials here: https://galaxyproject.org/learn/ - Also see the Variant analysis and VCFTools tool groups (at http://usegalaxy.org) or search for these in the Tool Shed.

The Cloudmap tool/pipeline as hosted on the same server is also deprecated. This workflow as originally created does make use of GATK. I am unsure if the Cloudmap authors have an updated pipeline. But you could contact them and ask if still supported, what the availability of updated workflows is, and which replacement tools to install into a local/cloud Galaxy to use the revised pipeline(s) (if exist). Contact information is here: https://usegalaxy.org/u/gm2123/p/cloudmap

Hopefully, this helps! Jen, Galaxy team

ADD COMMENTlink written 10 days ago by Jennifer Hillman Jackson22k
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