I've been having some issues with DP following CombineVariants:
I have two vcf files called by different callers - one by GATK UnifiedGenotyper and the other by samtools mpileup.
When I merge the files using CombineVariants, I notice that the DP per each variant is actually equal to the sum of DP of each of the vcf files. For example: If for a shared variant in both vcf files the DP=8, then the DP in the union file will be DP=16. Neverhteless, if a given variant is not shared by both files, then the DP in the union file will be equal to the input file.
Is there a way resolve this issue?