GATK 2.7.4 -mbq and HaplotypeCaller

mstagliamontemstagliamonte USAPosts: 12Member

Dear GATK Team,

I am trying to run HaplotypeCaller using GATK 2.7.4. I am getting the following error message:
ERROR: Argument with name 'mbq' isn't defined.

Here is my command line:
java -jar path_to_GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R path_to_reference.fasta -I reduced_01.bam -I reduced_02.bam -o combined_calls.vcf -stand_call_conf 30 -stand_emit_conf 30 -mbq 30

I am not sure what I am doing wrong. The algorithm is currently running as I just eliminated the -mbq parameter.

Regards,
Max

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,122Administrator, GATK Developer admin

    That's odd; I checked the code, that argument was present with the same name in version 2.7. Try using the long name --min_base_quality_score and see if that goes through. But there's no reason why this shouldn't work that I can think of.

    Geraldine Van der Auwera, PhD

  • mstagliamontemstagliamonte USAPosts: 12Member
    edited March 2014

    Hi,

    I've just tried to run it with the long name, but the result is the same. I am running the program on a computer cluster, maybe I need to report this to the admin.

    Thanks for your help,
    Max

    Post edited by mstagliamonte on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,122Administrator, GATK Developer admin

    Max, maybe try this with the latest version and see if the issue persists, just in case there was something off in the 2.7 version you're using.

    Geraldine Van der Auwera, PhD

  • mstagliamontemstagliamonte USAPosts: 12Member

    Thanks, I've just done it using v. 3.1.1 and got the same error.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,122Administrator, GATK Developer admin

    If you have a local machine available, you can try running on that and see if it's environment dependent...

    Geraldine Van der Auwera, PhD

  • mstagliamontemstagliamonte USAPosts: 12Member

    ... Thanks to the both of you. Just read Alex's answer. Sorry to have wasted your time, I read the script several times and still missed the typo.

    Kind Regards,
    Max

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