Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.

VariantRecalibrator accepts only one VCF file?

tommycarstensentommycarstensen United KingdomMember ✭✭✭

The documentation on VariantRecalibrator reads:

--variant  -V   []  One or more VCF files containing variants

However, when I supply multiple VCF files I get this error message:

A USER ERROR has occurred: Invalid argument 'out_GenotypeGVCFs/2nd.vcf.gz'.

Previously one could do --input vcfs.list. Now it seems the VCFs have to be merged prior to running VariantRecalibrator? Thanks!


Sign In or Register to comment.