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Hi,
I am wondering if anyone has ever come across this GATK error during the VariantRecalibrator step
I am wondering if anyone has ever come across this GATK error during the VariantRecalibrator step
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Last edited by medalofhonour; 10-09-2013, 10:26 AM. -
Yes, I've seen it. The error message says "Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself." so I had assumed that it was my mistake, something wrong with the command line. I reran VariantRecalibration with only the minimum of annotations, e.g. -an BaseQRankSum -an FS, and the error went away, so I assume it is when you are trying to use an annotation which only has minimal representation/information in the training variants in the input callset.
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