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Warning messages when perform GenotypeGVCFs


I am running a variant calling analysis using GATK 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!


  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    edited March 12


    I have to check with the team and get back to you. Usually this only happens when there are less than 10 samples present.


    EDIT: The developer says this could happen when a lot of the samples are low coverage and end up no-call. Can you check if this is the case? Thanks

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