Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
WARN messages with Haplotype Caller
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