Question: Variant Recalibrator in Galaxy
gravatar for smohapatra
3.7 years ago by
smohapatra0 wrote:

Hi, I am trying to run Variant recalibrator for SNPs and indels separately. Both the times I get this error :

"Argument with name 'qualThreshold' isn't defined"

I have used ref genome hg19 which I have used throughout my alignment process. I have used downloaded hapmamp, omni and dbsnp from GATK to use with galaxy after selecting the variants using the "Select Variants tool" from GATK after getting the raw vcf after using Unified Genotyper. The rest of the parameters are default given in galaxy. Can you please guide me in that ?


galaxy • 997 views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by smohapatra0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This is a GATK error - I would search their forum for the specific solution, then implement that on the Galaxy tool form. 

Sometimes errors are specific (it could be that the wrapper does not cover this particular parameter). Other times the errors are secondary to the root problem (missing or malformed inputs or usage/tool form setting's conflicts). Format and usage are the most common reasons for GATK tool errors (and most other tool errors).

If you do find that this is a persistent bug and that the wrapper seems problematic - after reviewing the help at GATK - please submit the error dataset as a bug report. 

Note that bug reports can only be sent in from the public Main Galaxy server. If you are not working there, see if the issue can be duplicated and submit if the problem is persistent.

This will also help to diagnose if the problem is with the tool wrapper itself or potentially another server's configuration for this installed tool. There are a few versions of GATK tools - if working on another server: you can compare what is on Main, those in the Tool Shed, and what is on the other server, which can also help to isolate where issues may be (if they are not due to usage/formatting).

Best, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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