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

No Output from GenomicsDBImport

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    Genevieve Brandt (she/her)

    Hello vivekruhela,

    Thanks for reposting! I have created a ticket on our github repository because I was not able to get to the bottom of this issue. You can see it here and follow along with what the developers discuss. I'll try to keep you informed when there is more information.

    Genevieve

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    Genevieve Brandt (she/her)

    Hi vivekruhela,

    Thank you for joining in on the discussion on github to help us find the issue quickly! When doing the liftovers you will want to make sure that all the naming conventions are consistent. I would recommend re-doing the liftover instead of just changing the chr, so you don't run into any issues.

    We don't maintain the UCSC files so I am not sure the best one to use.

    Glad that we were able to figure out the error message, let us know if you need anything else!

    Genevieve

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