I am running the VariantRecalibrator on GATK-3.4-46
But I get an error
ERROR MESSAGE: Bad input: Values for SOR annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
But my input vcf file has SOR annotation, so....what this error means?
I had been ran this process success before. Is it change something on 3.4-46 version?