VariantDatasetCombiner - dataset contains both multiallelic variants and duplicated loci for review

There is not currently a way to filter GVCFs during combination (I’ve created an issue for this).

Can you confirm that your GVCF file has multiple lines with the 302 locus? Do you know if Dragen has a configuration that prevent this?

In the short-term, I think your best bet is to filter the GVCFs by hand with awk or something. Apologies!