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

Could not find walker with name: DepthOfCoverage


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    Gökalp Çelik

    Hi Kayleigh Ostberg

    It seems that you are using an older version of GATK with an unsupported java version. GATK3 releases use JDK 1.8. If your JDK version is above this version then you cannot get GATK3 tools to run properly. DepthOfCoverage tool has been ported to the latest GATK4 versions albeit with reduced functionality here and there, but if that functionality is enough for you given that you check the commandline parameters and see if you hit any regression then I suggest you to try the latest GATK4 versions for your purpose. Otherwise it might be the best for you to get java 1.8. 

    I hope this helps. 


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