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

PathSeq freezing


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    Mark Walker

    Hi John Perkins,

    BWA will use off-heap memory to load the microbe index, so you want to make sure you have plenty of headroom for that. I'd suggest reducing the Java heap memory to the total memory less the size of the index, plus a little extra for the OS (a few GB). You may be running into garbage collection problems causing it to freeze.

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