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.

Re-starting GenotypeGVCFs from certain position?


I was joint genotyping about 400 samples with GenotypeGVCFs when I had node failure. The run was at about 83% which two weeks to get there. Is there a way for me to continue from this position rather than re-start the entire joint genotyping process? Thanks.



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Unfortunately, you will have to re-start your run. There is no way to ensure you will get correct results without restarting. Perhaps you can try running per-chromosome then merging the VCFs, so these failures will not affect you so much?


Sign In or Register to comment.