If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?