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GATK 3.8: Allele-specific Annotations

shalabhsumanshalabhsuman NIHMember
edited April 2018 in Ask the GATK team

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.

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