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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Values for InbreedingCoeff annotation not detected for ANY training variant

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    Pamela Bretscher

    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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    Vincent Appiah

    Hi Pamela Bretscher

     

    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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    Genevieve Brandt (she/her)

    Hi Vincent Appiah,

    Did you yet try to run VariantAnnotator to annotate the INDELs?

    Best,

    Genevieve

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    Vincent Appiah

    Genevieve-Brandt-she-her. I guess I have to annotated with Mills_100G_standard_indels file.

     

    Vincent

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    Vincent Appiah

    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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    Genevieve Brandt (she/her)

    Oh I see! I'm glad you found a resolution, thanks for posting your solution.

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