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Problem with ApplyVQSR: output.AS.tranches file empty

gspiritogspirito Member
edited August 19 in Ask the GATK team

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,

Giovanni

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