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Question: GATK and c. elegans
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gravatar for peadams
22 months ago by
peadams • 0
peadams • 0 wrote:

Hey,

Has anyone ran C. elegans data through GATK? I have the dbsnp file but am stuck on the Variant quality score recalibration step (VQSR). For this step you need more than just the dbsnp variant file, but I haven't been able to find anything helpful. Any tips would be appreciated.

Thanks
c elegans dbsnp gatk • 698 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by peadams • 0
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

In short, the tool requires a specific type of annotation input. If you are using the newer GATK tools wrapped for Galaxy, the basic protocol for line-command use described in the help links below is the same as the Galaxy use (the underlying tools are the same).

The GATK tools at Galaxy Main (http://usegalaxy.org) are from version 1.4 and deprecated. Newer versions of the wrapped tool suite are available in the Tool Shed for use in a local or cloud Galaxy (https://wiki.galaxyproject.org/BigPicture/Choices).

Hopefully this helps, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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