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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

GATK Runtime Error 3.8

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    Tiffany Miller

    Hi Nicholas Cho Rui Wen - your best bet is to upgrade to a newer version of GATK. The team only supports issues related to GATK 4. Sorry about that. 

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    Nicholas Cho Rui Wen

    Dear Ms. Miller,

    Thank you for your reply. I know I might be detracting but I actually ran GATK4.0 for a separate analysis but it is rather slow as I am using the local.jar file which does not have the -nct option. I understand that the GATK4.0 spark.jar file has that option but it is still in beta mode and I understand that the GATK team cautioned against using the spark.jar file for generating results for publication. May I know when the spark.jar file will be in full operational mode? Please advise me. Thank you.

    Yours Sincerely,
    Nicholas Cho

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    Tiffany Miller

    I see your issue. Is the speed something that can be sacrificed in order to use a better version of the tool? I'll see if I can find anything more about the Beta status of HaplotypeCallerSpark.

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    Nicholas Cho Rui Wen

    Dear Ms. Miller,

    Thank you for your reply. Ideally, I would want the speed to be fast, and this is because on GATK 4.0, one samples take about 3 days to run, even when using the "--native-pair-hmm threads 50" option, but I'll discuss this with my principal investigator. Thank you for checking on the Beta status of HaplotypeCallerSpark.

     

    Yours Sincerely,

    Nicholas Cho

     

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    Tiffany Miller

    Hi Nicholas Cho Rui Wen

    We are prioritizing other work over getting HaplotypeCallerSpark out of Beta and we don't have a timeline for doing that yet. As you said, we need to do a formal evaluation for correctness before officially endorsing it. Sorry, I don't have any more specific timeline to share at this moment. 

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