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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

java.lang.OutOfMemoryError using BaseRecalibrator

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    Genevieve Brandt (she/her)

    Thank you for posting this solution WangZiwei! Did you ever determine why the original file was causing the error? If you identified the exact cause, then I could put in a feature request to add a check for that type of problem.

    I'm glad you were able to find a solution!

     

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    WangZiwei

    Hello Genevieve Brandt (she/her)

    perhaps Mills_and_1000G_gold_standard.indels.hg38.vcf.gz(.tbi) caused the problem, because when I redownloaded it from GATK resource bundle, the error just dissapeared.

    I guess the file might have been broken, which is a little bit strange since the file has been used before.

    The solution is not expected so I forgot to keep the original file for further examination. Sorry for that.

    Regards,

    Wang.

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    Genevieve Brandt (she/her)

    That makes sense. I'm glad you got it fixed quickly!

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