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

GATK BQSR is taking too long to be run (running since last 6 days)



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    Gökalp Çelik

    Hi Niharika

    How many reads do you have in that bam file? Also can you share the specs of the compute environment that you are running this tool? 

    It is possible that the java VM is actually hung and the tool itself is not doing anything at all.

    Can you provide us more information about these matters?


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    Using sorted bam solved my problem

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