Test-drive the GATK tools and Best Practices pipelines on Terra
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HaplotypeCaller error: Argument with name 'mbq' isn't defined
I ran HaplotypeCaller with the following command
java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T HaplotypeCaller -minPruning 3 -R genome.fasta -I reduced.bam -o Chr10.vcf -stand_call_conf 50 -mbq 20 --dbsnp /home/bioinfo/data/genomes/rice/nipponbare_v7.0/variations/all_sorted.vcf
and it gave the following message with the error:
ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
ERROR MESSAGE: Argument with name 'mbq' isn't defined.
I was wondering what am I doing wrong. I see that -mbq is defined in the haplotypeCaller page. Was it not defined in the version 2.8.1?