any plan to provide other variant caller tools ?

Question: any plan to provide other variant caller tools ?

3.8 years ago by

BC357 • 70

United States

BC357 • 70 wrote:

From what I could find, Galaxy currently provides Varscan and UnifiedGenotyper for variant calling. It appears that there are other tools available and some seem to outperform Varscan and UnifiedGenotyper. For example, GATK's Haplotypecaller is recommended over UnifiedGenotyper, although it does seem to take more computer power to run. Other tools such as Platypus, SGA, DISCOVAR, Scalpel also have good online reputation, although I do not know how extensive these tools have been tested. Platypus does have one publication out and it seems to be a fast and lightweight tool. Is there a plan to provide them (?not sure if this is the correct verb) on Galaxy main server?

variant caller • 956 views

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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by BC357 • 70

You mean provide in usegalaxy.org or in the Galaxy ToolShed. A few of your mentioned tools are available from the Tool Shed.

ADD REPLY • link written 3.8 years ago by Bjoern Gruening ♦ 5.1k

I meant usegalaxy.org

ADD REPLY • link written 3.8 years ago by BC357 • 70

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Freebayes and Naive Variant Caller are on the public Main Galaxy instance at http://usegalaxy.org. Going forward we cannot comment yet about additional tools, although I can let you know that the core tool set to be supported on the Main server is under review at this time.

Some of the variant analysis tools under review can be found on the public Test Galaxy instance at https://test.galaxyproject.org.

The Tool Shed is a good resource, as mentioned before (for use in a local or cloud Galaxy). As can be other public Galaxy instances hosted by other groups. Choices for how/where to use Galaxy, with links to resources/how to set up (when needed), can be found in our wiki here:
https://wiki.galaxyproject.org/BigPicture/Choices

In addition, most any 3rd party tool can be wrapped and used within Galaxy (in a loca/cloud), if you have resource to do that.

Hopefully this helps some more, Jen, Galaxy team

ADD COMMENT • link modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you very much for the update! Will take a look at Freebayes and Naive Variant Caller. In my limited experience, using Tool Shed in a local or cloud Galaxy requires more resources and computer know-how. usegalaxy.org on the other hand has an easy interface that allows non-bioinformaticians to get the job done, which provides the needed "buffer time" for non-bioinformatician to learn how to do it bioinformatically.

ADD REPLY • link written 3.8 years ago by BC357 • 70

Glad that helped. To get familiar with both of these tools, this tutorial covers both, including the data prep steps:
http://usegalaxy.org/u/galaxyproject/p/galaxy-101-ngs-variant -Jen

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

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