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Variant Recalibration failing
I'm trying to run variant recalibration for SNP as part of the GATK best practice workflow for DNA sequence analysis but am getting the following error presumably because after training there are 0 variants with an LOD score <= -5.0.
The error is:
ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result
Caused by: java.lang.IllegalArgumentException: No data found.
... 5 more
I am using GATK 3.2-2. The full output from this stage is attached.
I also got a similar error with GATK 3.1. I have run it a few times now and although there are very slight variations in the numbers it outputs the result is consistently 0 variants with a LOD <= -5.0.
I have run this stage successfully when I process my reads in two separate chunks but when a combine them all into one processing pipeline they fail at this stage.
Any advice would be welcome on to analyse this and determine what I need to change or where I am going wrong.