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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 - KEY END found in VariantContext field INFO but this key isn't defined in the VCFHeader

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    Pamela Bretscher

    Hi Ryan Sun,

    It looks like your VCF header may be missing a declaration of the "END" INFO field which is causing the error. Can you take a look at this similar post which shows the potential solution: https://www.biostars.org/p/371307/. Please let me know if this is helpful.

    Kind regards,

    Pamela

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    Ryan Sun

    Hi Pamela,

    Thanks for your response. I followed the suggestions of that post, and manually added END tag to VCF header. It worked but ran into other problems later.

    One person in Github gave me a reminder about this issue and I carefully checked best practice again, finding the CombineGVCFs must take gVCF (genomic VCF) files as input. Unfortunately, I used normal VCF files (forgot to add -ERC GVCF in HaplotypeCaller step). I tried again and it worked well this time.

    Anyway, I really appreciated your time and effort!

    Ryan

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    Pamela Bretscher

    Hi Ryan Sun,

    Okay, I'm glad to hear that was successful and that you were able to get HaplotypeCaller to work as well. Are there any issues that you are still experiencing that I can help with?

    Kind regards,

    Pamela

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