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--defaultBaseQualities in Haplotype caller

Dear Team,
I'm getting the following error in Haplotype Caller (2.8-1):

argument --defaultBaseQualities has value -1.00, but minimum allowed value is 0.0

while according to the CommandLine documentation the default value should be -1.
I'm running GATK through Galaxy, where all the inherited arguments (including --defaultBaseQualities) and their default values are common to all the tools, and I only received this error with HaplotypeCaller.

Regards,
Paolo Uva

Tagged:

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Ah, I did not know that about Galaxy, good to know. Not sure about the HC's handling of DBQs but basically if you have bases without qualities you'd probably want to throw them out anyway, so 0 should do just fine.

    I will definitely fix the checking system so this no longer happens. I can't promise to get it done for 3.0 because I'm overcommitted right now, but I'll do it asap.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Paolo,

    I'm sorry, that's a bug due to a new feature we put in to safety-check that the values of arguments are in range. I forgot to add an escape clause for out-of-range values that disable certain behaviors. I believe this should only happen if you are setting the argument to -1 at the command line rather than letting the default value be set internally. Can you check the command line that is generated to see if the one for HC explicitly sets this value to -1?

  • Hi Geraldine,

    you are right! The command line generated by the Galaxy wrapper for HC explicitly sets the value to -1. This happens because when selecting the advanced options of the GATK tools in Galaxy, all the parameters are sent to the command line explicitly with their default values.

    As I cannot leave this parameter empty in Galaxy, at the moment I manually set --defaultBaseQualities to 0 (assuming this is equivalent to the default value internally set by HC).
    However, it would be nice for the future release to let HC accept the same default values used by the other GATK tools.

    Paolo

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Ah, I did not know that about Galaxy, good to know. Not sure about the HC's handling of DBQs but basically if you have bases without qualities you'd probably want to throw them out anyway, so 0 should do just fine.

    I will definitely fix the checking system so this no longer happens. I can't promise to get it done for 3.0 because I'm overcommitted right now, but I'll do it asap.

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