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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

GATK 3.4-46 producing v4.2 VCFs?

just a tiny question. I am using GATK in current version 3.4-46 for "joint variant calling".
A subsequent "snpEff" job on the resulting VCF file complained about a weird genotype in ALT column.

In prior versions of GATK (3.4.0) there were <*:DEL> but in the current version there is a * instead.
The * has been introduced with VCF version 4.2. So it seems current GATK writes v4.2 VCF files. Can you confirm that?
If so, then the VCF header is not correct, it shows ##fileformat=VCFv4.1 .


Issue · Github
by Sheila

Issue Number
Last Updated

Best Answers


Sign In or Register to comment.