It seems all recent GATK's HaplotypeCaller versions (versions 3.2 to 3.6, haven't tested older versions) miss to generate some of annotations like FS and QD (even when requested explicitly by --annotation flags) when they are used in gVCF mode. UnifiedGenotyper consistently generate these. This causes the later VQSR steps to fail in learning phase (if it's set to use these annotations).
Could you please let me know if this is intentional and if there is any resolution for this issue?
Thank you
Amin Zia