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.
Notice:
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.

vcf / GVCF result sets differ

Hello,
It seems that running HaplotypeCaller with -ERC GVCF and then running GenotypeGVCFs -stand_call_conf 30 -stand_emit_conf 30 gives a different vcf than HaplotypeCaller -stand_call_conf 30 -stand_emit_conf 30 (on a single sample). Is that expected? I tried versions 3.2 and 3.5.

Tag along question: I've tried to be a good citizen and post questions on existing topics in this forum (instead of starting yet a duplicate thread) but these never get answered. Is it always better to post a new question?

Thanks for your help.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    We aim to answer everything regardless of where it gets posted. You may have been unlucky and posted hard questions at especially busy times... I'll be going through our backlog over the weekend and will try to catch up on any unanswered questions.

    For this one, in a nutshell, minor differences are expected, but nothing major. Did you quantify the differences you observed?

Sign In or Register to comment.