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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

CombineGVCFs - A USER ERROR has occurred: Bad input: Raw value for annotation has 1 values, expected 2

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    Genevieve Brandt (she/her)

    Hi David Medina,

    Do you know how these VCFs were created? It looks like there is an issue in your RMSMappingQuality annotation. 

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi David,

    We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!

    Kind regards,

    Genevieve​

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    David Medina

    Hi,

    I am not sure how this VCF was created. I ran the process again and it seemed to solve the problem. However, I would like to know if there was any other plan of action I could apply in order to "fix" the wrong RMSMappingQuality annotations.

    Thank you,

    David Medina

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    Genevieve Brandt (she/her)

    Hi David Medina,

    Unfortunately, there isn't a better way to do this. The RMSMappingQuality annotations are annotated by the mapper and cannot be re-annotated in GATK if they are missing.

    Best,

    Genevieve

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