Hi all, With GATK4.3.0 I try to use VQSR and I got the error message. Based on GATK tem recommendations, I ran "VariantRecalibrator model" to fix the error https://gatk.broadinstitute.org/hc/en-us/articles/9570271608219-VariantAnnotator. However. the error message still persists. Is there any other way to fix such problem? Thanks!
A USER ERROR has occurred: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
Dear Pierre Lindenbaum, So, is there any way to fix and proceed the SNP calling process? I am quite new for such kind of analysis.