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GenotypeGVCFs: --includeNonVariantSites disappeared?
I just wanted to use the GenotypeGVCFS tool to genotype some gvcfs at known variant sites and am also quite interested if my samples are reference at these positions or if the sites are not covered. The old GATK 3.7 version had the option --includeNonVariantSites, which is not supported by GATK4... Do you have some hints or a workaround? Currently, I'm rolling back to v3.7 which might lead to difficulties later.
Thanks for your help