Values for InbreedingCoeff annotation not detected for ANY training variant
Answered
When I use gatk VariantRecalibrator module to call germline mutation, a error occurred:
A USER ERROR has occurred: Bad input: Values for InbreedingCoeff annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
I called germline mutation (WES data) as documented by offical web step by step from HaplotypeCaller →GenomicsDBImport →GenotypeGVCFs →VariantRecalibrator ， the first three steps operated successfully, except the VariantRecalibrator, error occurred as as above mentioned.
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Hi chenglei,
VariantRecalibrator requires that the variants in your input VCF file are annotated to build a model of how likely each variant is to be a true variant. It seems you are getting this error because your variant file has not been annotated. Can you run VariantAnnotator on your VCF file and then re-run VariantRecalibrator to see if this gets rid of the error?
Kind regards,
Pamela
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I have a similar problem. In my case, running VariantRecalibrator in SNP mode works but INDEL mode gives the error message given by chenglei
Please advice.
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Hi Vincent Appiah,
Did you yet try to run VariantAnnotator to annotate the INDELs?
Best,
Genevieve
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Genevieve Brandt (she/her). I guess I have to annotated with Mills_100G_standard_indels file.
Vincent
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Genevieve Brandt (she/her) I resolved the issue. Looking the GATK best practises , I realised my command was not working because I had less than 10 samples. I had to remove the -an InbreedingCoeff option. And the command worked.
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Oh I see! I'm glad you found a resolution, thanks for posting your solution.
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