Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

BaseRecalibrator --max-cycle


1 comment

  • Avatar
    Genevieve Brandt (she/her)

    Hi oğuzhan karaosmanoğlu,

    If you have enough memory, you can increase the value if you would like. More cycles could potentially help the model, but unless you are having issues with the model, I don't think you need to change the default. We usually optimize the memory requirements so that the tools do not require too much memory while still getting good results.

    Also, make sure you are only specifying the argument name once. You don't need to write --maximum-cycle-value -max-cycle 5000, just --maximum-cycle-value 5000. One other note probably unrelated to your issue is that we recommend using the GATK wrapper script instead of calling the jar file:



    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk