Warning messages when perform GenotypeGVCFs

Hi,

I am running a variant calling analysis using GATK 4.0.1.2 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!

Answers

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