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.

GenotypeConcordance printInterestingSites argument

MarthaMartha CracowMember

I didn't find the answer anywhere, so I'm asking here.
I'm using GATK 2.6-4. I used GenotypeConcordance to compare two datasets, and it was great, exactly what I needed. But then, I was interesting in the discordant sites, and I saw that printInterestingSites should be a good solution. But I can't make it work. Just adding in my command line "-sites filename" doesn't work, and I've tried to be creative in changing this option. Then I thought, that maybe this option isn't working in my GATK version.
Have I just done something wrong?

Best Answer


Sign In or Register to comment.