If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
Problem with ApplyVQSR: output.AS.tranches file empty
Hello, I run into a problem with ApplyVQSR:
I run the GATK4 best practices on 45 WES trios, for most trios I have no problem and the analysis ends with no errors. However for 7 out of 45 trios the VariantRecalibrator generates an empty output.AS.tranches file, therefore the following command (ApplyVQSR) fails:
A USER ERROR has occurred: No tranches were found in the file or were above the truth sensitivity filter level 99.0
I don't think the problem is in the commands I use, since I have no problems for most of the samples. Also other than the error above, this issue is not associated to any other error or warning.
I wanted to ask what could be the reason for an empty tranches file and how to possibly overcome this issue.
Thank you in advance,