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Require Genotypes in VCF file in order to output Fst statistics
I am using a VCF file obtained from "GenotypeGVCFs" to calculate Fst statistics with VCF tools.
I get this error message:
Error: Require Genotypes in VCF file in order to output Fst statistics.
I suppose something went wrong when creating the VCF file with GATK:
I first used "HaplotypeCaller" for
-ERC GVCF cohort analysis workflow; and then I combined all the resulting gVCF files into one with "GenotypeGVCFs".
So, an idea about what this error message means?