Hi,
I began a run using the --emitRefConfidence GVCF command asking for a .g.vcf file to be output for a single sample. Which is running (yay)!
So far, it is still running and has thrown up several warning messages. Two of them I understand, but these two I am not sure about. Can anyone throw some light on these for me please?
WARN 18:42:38,322 AnnotationUtils - Annotation will not be calculated, genotype is not called
WARN 18:42:38,342 AnnotationUtils - Annotation will not be calculated, genotype is not called
WARN 18:42:38,358 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not HaplotypeCaller
Many thanks,
Jenni