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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 conda install issues

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    Gökalp Çelik

    Hi Thomas Stevens

    It seems that this issue has just started to affect gatk conda environment installations especially a certain amount of time passes after a gatk stable release. I will check with our team to find a permanent solution to this issue. In the meantime you may want to use docker image for gatk which includes all the required dependencies in a single package. 

    I hope this solves your issue at least temporarily. 

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    Thomas Stevens

    Thanks, I unfortunately can't currently use docker with the HPC system. But, I can try to find a solution to that if I can't fix the conda method. 

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    Gökalp Çelik

    Hi again.

    Can you check the version of Conda you are using? Using very outdated versions may also cause this issue. Sometimes updating conda installation and rebuilding the environment from scratch can solve the issue. If not let us know. 

    Regards. 

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