Combining RAW_MQ and MQ

Hi,

I have two batches of gvcfs :
- one was processed using GATK-3.3
- one was processed using GATK-3.5

I want to perform a joint calling + VQSR using both batches together. The problem is that the batch from GATK-3.3 has the MQ annotation while the other from GATK-3.5 has the RAW_MQ annotation.

Can the GenotypeGVCFs of GATK3.5 handle both MQ and RAW_MQ to compute a unique MQ value that can be used by VQSR ?

It seems that VariantAnnotator and CombineGVCFs cannot add the MQ annotation to the gvcfs from GATK-3.5 (using the -A parameter).

Best