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Warning messages when perform GenotypeGVCFs
I am running a variant calling analysis using GATK 18.104.22.168 suite on 25 human subjects. After I use CombineGVCFs to have a single gvcf file and run GenotypeGVCFs, the log repeatedly shows
WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
for several hours. I have opened the combined gvcf from CombineGVCF and confirmed I have all samples in it. For the function arguments, I am using defaults.
Since this repeatedly shows up, I wonder if this is normal.
Thank you very much!