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HaplotypeCaller - Genotype Given Allele Mode
I want to call variants for some samples using Genotype Given Allele mode(GGA) of HaplotypeCaller. I have used UnifiedGenotyper earlier in GGA mode.
I am not sure about the right approach to do GGA mode in HaplotypeCaller.
You make GVCFs for all BAMs using HaplotypeCaller in GGA mode and later use the GenotypeGVCFs walker to make VCF from these GVCFs. Is this the way to do this ?
Or Since GVCFs has all the sites from BAMs, can GenotypeGVCF can do a variant calling using GGA mode. I know that the GenotypeGVCF doesn't have the GGA option currently. But just checking the right approach.