Various target performance tweaking

lletourn

Hello, 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.

Thanks Louis

Geraldine_VdAuwera

Hi Louis, we don't currently have such a page, but we are working on a document that gives tips on how to improve performance for the main processing and calling tools. It should be ready in a couple of days.

lletourn

Excellent, looking forward to the Document.

Thanks for the great work.