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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
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,