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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

Error when running HaplotypeCallerSpark

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    Genevieve Brandt

    Hi Jeongmin Bae, thank you for reporting this issue. Could you test that this crash occurs if you run on a different machine with the same data? Could you provide a minimal file that triggers the crash and upload it following these instructions? Please include the BAM and the reference files.

    I have found a related issue on github and commented your example there. You can track that link for more updates.

     

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    Jeongmin Bae

    Thanks for the reply. I sent the related files.

    I hope this problem will be solved.

    Thanks!

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    Genevieve Brandt

    Hello Jeongmin Bae, thank you for sending those files. Have you tested to see if the crash occurs on a different machine with the same data?

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    Jeongmin Bae

    Yes, the same crash occurred in different machine. Even if it works well when I run HaplotypeCaller (not SPARK version), the crash occurs in the case of spark version. Is there a problem when using the docker environment?

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    Genevieve Brandt

    Hi Jeongmin Bae, thank you for confirming that. It looks like this is a bug with HaplotypeCallerSpark and not an issue with the docker environment as far as I know, but you can see any updates at the github link that I sent. 

    HaplotypeCallerSpark is still in BETA, and so generally, we would recommend that you use the normal HaplotypeCaller. HaplotypeCallerSpark has not been tested as rigorously as the normal HaplotypeCaller and may have issues, such as this one. You can still parallelize the normal HaplotypeCaller using intervals.

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