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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

There are 2 comments on this article. To see them or add your own, view this post on the forum