I am using GATK-3.8.1 for HaplotypeCaller (using gVCF mode and then GenotypeGVCF) and I noticed that final VCF output from GenotypeGVCF has missing DP values.
I found a workaround that while doing gVCF calling if I skip the -G StandardAnnotation -G AS_StandardAnnotation parameters, but then if I keep those parameters during the GenotypeGVCF step, DP values are NOT missing anymore.
My question is if the values for 'Allele-specific annotations' in the Final VCF will be any different if you don't include those -G parameters while gVCF calling but include them during GenotypeGVCF mode COMPARED to when you include those during both steps (gVCF and GenotypeGVCF steps) ??
*I am not able to upgrade to GATK-4 yet, since we still want to utilize UnifiedGenotyper feature.