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.
GATK 4 GenotypeGVCFs tool does not accept multiple GVCF files?
I have migrated from GATK 3.7 to GATK 4 tools for my whole genome and whole exome pipelines. I am using the alignment data for a family trio (aligned by BWA-MEM). Following the best practices, I run HaplotypeCaller in GVCF mode and put all three GVCFs (for mother, father and child) through GenotpyeGVCFs tool. The error I'm getting is the following.
A USER ERROR has occurred: Argument '[V, variant]' cannot be specified more than once.
which is very strange because GenotypeGVCFs tool is designed to work with multiple GVCFs. Also, the documentation for this tool uses it exactly with multiple variant arguments.
GATK 3.7 version of GenotypeGVCFs works just fine with those arguments, so I'm currently using that. However, I would like to switch to version 4.
Is this a bug in the GATK 4 beta version?
Thanks a lot!