Various target performance tweaking

lletournlletourn montrealPosts: 6Member
edited November 2012 in Ask the GATK team

I was wondering if you have a page that explains which parameters affect performance of which tragets of the GATK?

In particular

  • DepthOfCoverage
  • RealignerTargetCreator
  • IndelRealigner

For whoel genome, DepthOfCoverage can take more than 30hours and this is with the ommit base counts. Would putting in a higher read_buffer_size with more ram help, etc.


Post edited by Geraldine_VdAuwera on

Best Answer


  • lletournlletourn montrealPosts: 6Member

    Excellent, looking forward to the Document.

    Thanks for the great work.

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