Genome Analysis Toolkit

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

Trio Denovo annotation using VariantAnnotator PossibleDenovo not working?


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    Bhanu Gandham

    Hi Jan,

    I apologize for the delay in getting back to you. I was attending a conference.

    Can you please try the latest version of GATK which is v4.2.2.0. The version you are using is quite old at this point. So just updating your version might solve this issue.

    But if you are still not seeing any variants annotated as hi/loconfdenovo even with the updated version, then please share a few variant records from your input vcf that follow the rules for those annotation. The rules are provided in the header — ##INFO= 

    = 20 for all trio members)=[comma-delimited list of child samples]">

    ##INFO== 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]">

    It would be helpful if you could provide some variant records from the input that follow those rules and the same set of the variant records in the VariantAnnottator output vcf. This will help me debug the issue.

    — Bhanu

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