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Meaning of warning (<10 samples for inbreeding calculation) while joint genotyping (GenotypeGVCFs)
I have combined my gvcfs produced by HaplotypeCaller into one vcf file using CombineGVCFs.
When I use said vcf file for joint genotypeing with GenotypeGVCFs, I get often the following warnings:
WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples
This is makes me wonder if I have done the previous steps correctly, so I will give you some background to what I am doing.
1/ We are working with 6 different lines of mouse
2/ For each line, 10 animals were sequenced.
3/ Variants were called per sample with HaplotypeCaller in GVCF mode (after preparing BAMs as per GATK's best practices)
4/ gvcf files were combined with CombineGVCFs regardless of group membership (60 gvcfs)
5/ Joint genotyping with GenotypeGVCFs
I am now wondering if the fact that on step 4 I did not produce one combined vcf per group (i.e. 6 vcfs, each resulting from 10 gvcfs) could have something to do with this warning.