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How to includeing loci of non-variant in GenotypeGVCFs step with GATK4?
I called germline short variants using haplotype caller with GATK 4.0, and then I want to extracted the non-variants and variants ** into seperate files so I could filter them seperately. In the GATK 3.x pipeline, there used to be **-allSites or --includeNonVariantSites in GenotypeGVCFs . Is it there no more in this new version?
Thanks in advance~