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

PathSeqBwaSpark Follow

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    Amir Hozhabrpour


    I run  PathSeqBwaSpark on a server with about 140 G RAM and 12 threads. 201 hours or about 8 days have passed so far but this part is not finished. I don't know why, but the server uses only one core, but it changes between 12 cores and the CPU is running at about 95%.

    i run this part with human and microbiome files located in the gatk bundle and my input file is a bam located on the pathseq tutorial.

    If anyone can help me in this section, I would be grateful.


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