Question: HOW TO COMBINE VARIANTS IN CLOUDMAP IN GALAXY
1
gravatar for supinderkr
19 months ago by
supinderkr10
supinderkr10 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 • 409 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by supinderkr10
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson25k 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 19 months ago by Jennifer Hillman Jackson25k
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