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Why "InbreedingCoeff -must provide < 10 samples" warning is generated, when no. of samples is 29?

Dear GATK Team,

I tried performing joint calling for 29 samples from the genomicsDB datastore for the interval of complete chromosome 1.But got the following warning " WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples". Even though my number of samples is 29, stil the warning is saying must provide atleast 10 samples.
Also,in the generated vcf file I have the inbreeding score calculated and mentioned. Then Why am I getting this warning? Is it something to worry about?

Thank you

Regards

Abhishek

Answers

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @abhishekpanda ,
    This post explains that the "code throws this error when the tool does not count any sample where the genotype is null (./.) towards the sample count. So for your sites, those lacking the annotation will have fewer than ten genotypes." You shouldn't have to worry about this WARN. The team is working to resolve WARNs like this.

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