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# GATK 2.7.4 -mbq and HaplotypeCaller

USAMember Posts: 12

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

Tagged:

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

• USAMember Posts: 12
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.

Max

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

• USAMember Posts: 12

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