In variant recalibration (2)

Good day I am currently attempting to Build the VQSR model with raw indel variant data. However I have received the following error message
INFO 11:04:43,136 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.4-9-g532efad):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --percentBadVariants 0.05, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example)

It is the first time that I have come across such a message. Can someone explain what the cause of this error could be? and what effect changing these two suggested parameters would have on exome data indel variant recalibration?

Kind Regards

Best Answer


  • FourieFourie Member

    Dear Geraldine

    Thanks - much appreciated - that makes things a lot clear!

    We have been spending a lot of time with the documentation, but have not come across such a clear explanation.

    It can be quite tough to find the right info as the documentation is spread across several documents.

    Could you please point us towards the relevant section - it will hopefully prevent further such questions?

    Best regards!


  • FourieFourie Member

    PS For other persons reading the forum, this document also seems pretty useful: tutorial/VQSR tutorial.pdf

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Fourie,

    Glad that helped. We're aware that right now the documentation is a little confusing on this -- it's a complex topic. And looking up the docs to link the information I referred to here, I realized it's not explicitly spelled out anywhere. So I'll add this to the FAQs in the methods article about VQSR. In future we'll try to clarify things further and consolidate some the info. Thanks for the feedback!

  • FourieFourie Member

    Hi Geraldine

    Great - thanks!

    We found the FAQ which has very useful info, this would be a welcome addition!

    Best regards!


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