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Running costs on FireCloud

I'm trying to find out about how much it might cost to run a cohort of samples (500, 1000, or 2000) using germline GATK Best Practices Pipeline on FireCloud , and also how long the runs might take. Thanks

Best Answers


  • OluOlu Member
    Hi @SChaluvadi

    Thanks for your reply. Just one more question: What advice would you give me if I have fastq files to kickstart my analysis in fireCloud instead of uBAM?
  • OluOlu Member
    @SChaluvadi So can we can convert the uploaded fastq files to uBAM using the provided protocol in fireCloud. Is this correct?
    Just to be sure I understand the pricing correctly, I checked the pricing you mentioned and saw for example, GATK Best Practices for Germline SNPs & Indels analysis for one sample (e.g., NA12878):
    1-Processing-For-Variant-Discovery - 4.98
    2-Haplotypecaller-GVCF - 2.24
    3-Joint-Discovery - 0.90
    Total: $8.12

    I guess in addition to the total cost above, the storage costs after analysis (at-rest storing of data in Cloud Storage) will be based on Google cloud charges. Is this correct?

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Yes, you should be able to convert your fastq files to the uBAMs by following the tutorial.
    For costs, you will have to also factor in the size of your sample. In the example we provided, we noted the size of the NA12878 sample and the costs associated with each Tool based on the size. If your file is also of similar size, you can expect that this estimate still stands. Please keep in mind that these numbers are estimates since there are variables we cannot account for such as your storage costs after analysis etc.

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