The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
Bugfix: GCContent should be float instead of integer
Validating the vcf file which comes out of the VariantAnnotator is resulting in an error. The GC Content is a float and not an integer (which is stated in the INFO column).
At the moment we are do a search and replace ourselves, but it would be nice if it can be fixed in a next version of GATK.