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VQSLOD score and variant quality

Dear GATK team,

For VQSLOD score, can I understand it as way to rank variants. The higher the score, the more reliable the variant being true positive?

I have an output file from GATK 2, and there are some variants with low VQSLOD scores (e.g. -5), and being labeled as "Pass", while some other variants with higher VQSLOD scores being labeled as "VQSRTrancheSNP99.90to100.00". Do these results make sense to you?

Please let me know.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Sharon,

    Your interpretation of the VQSLOD score is correct. What you're observing in that VCF file doesn't make much sense to me. Is it possible that the VCF was produced by combining different files, or is this the direct output of ApplyRecalibration?

  • xhzhaoxhzhao Member

    Thanks a lot, Geraldine!

    I don't know exactly what happened, as this is provided me by others. But I think the file is processed by individual chromosomes, and combined later. I will check out. Thanks again!


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