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Using NIO with GATK4 HaplotypeCaller

breardonbreardon Cambridge, MAMember, Broadie

Is GATK4 HaplotypeCaller NIO compatible? If not, is there another version that is?


Best Answers


  • breardonbreardon Cambridge, MAMember, Broadie
    edited June 2018

    Great, thanks Sheila!

  • mikedamourmikedamour Member
    edited October 2018

    How can one tell if a WDL or tool is NIO compatible? Do I look at the WDL, the tool code, or just the version of Cromwell?

    The question comes down to which public workspaces or methods will give the NIO reduced-file-localization advantage. Should I assume any methods or workflows dated before Feb '18 don't use NIO? Are all later ones NIO-enabled? Where do I look to check?

    I used the Somatic_variant_discovery_hg38_v0 of 8/23/17 and saw it spending 1.5 hours localizing my (90X, 312GB tumor and 215GB normal) BAM files on each of 50 instances. Had to double the specified local disk size from 500GB to keep it from giving "unexpected termination" exception. Assume NIO will be a big win on this kind of run.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @mikedamour

    This seems to be more of a firecloud/workspace question so I will pass it on to that specific team and they will help you out with this question.


  • Oh thanks for the rapid response, Bhanu.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Hey @mikedamour -
    NIO is compatible with Cromwell 33 (and higher) and WDL 1.0 (or higher), though FireCloud has not adopted WDL 1.0 yet. However there is no simple way to determine which tasks are compatible with NIO. One way that you could tell would be to look in the code for cases where inputs are Strings whereas they would normally be Files (this only applies to GATK4 and above). Additionally, we could have someone on the team look at the specific method in question and help you determine its NIO compliance.

  • Hi Bhanu, how can I follow up on your referral to the firecloud/workspace team? Should I repost the question elsewhere?

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @mikedamour

    You can post your questions here. @SChaluvadi will help you out with it.


  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Hey @mikedamour, since we haven't heard any updates from you we will now be closing this ticket but please feel free to reply back with any follow up questions that you might have!

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