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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.