Recommended parameters for GenomicsDBImport

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Arye Harel

• October 25, 2020 07:26
• Edited

a)How do I use GenomicsDBImport for many files and following system criteria

Hi,

I need to use GenomicsDBImport  on ~250   *.g.vcf.gz  files which sum up together to ~5GB (each file ~10-20MB).

I can give this process: 50 cups and 400GB RAM on my linux cluster system.

 

What are the best parameters to run the GenomicsDBImport command for the above task?

    In specific, how many intervals should I use  (the -L param)?
    Is it recommended to use batch ( the --batch-size param)? if so, how many?
    If batch is used, what will be your recommendation for threading (--reader-threads) ?
    Would you recommend to use import intervals in parallel  (--max-num-intervals-to-import-in-parallel)? how  many?

 

Thank you,

 

Arik

 

 

 

 

 

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• 

  Genevieve Brandt (she/her)

  • October 23, 2020 21:51

  Hi Arye Harel, 

  Thank you for your question! This question falls outside of the scope of GATK Support. (See our support policy for more details). However, we encourage you to keep posting questions because they help us improve our documentation and build resources. In addition, if you know the answer to other questions outside of our GATK support team scope, please help out other users! And other users feel free to chime and discuss here.

  Your question may be already answered in our extensive documentation and forum.  Please see these resources for more information:

  • GenomicsDB ToolDocs
  • Extensive GenomicsDB Documentation
  • Using GenomicsDB with Intervals
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