Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Various target performance tweaking

lletournlletourn Posts: 2Member
edited November 2012 in Ask the team

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

Post edited by Geraldine_VdAuwera on
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