Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

Sign In or Register to comment.