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Bug in VariantRecalibrator

Hi there,

So for the SNV model in VariantRecalibrator, I was using QD, MQRankSum, ReadPosRankSum, FS for a little while and then decided to add MQ back in since I saw that BP was updated recently and that was back in for BP.

However; when I added MQ back in, and it went to train the negative model, it said it was training with 0 variants (same data set w/o using MQ in the model yielded ~30,000 variants to be used in the negative training model). I have attached a text file that has the base command line, followed by the log from the unsuccessful run and then followed by the successful run log. The version 3.1-1 and there are approx 700 exomes.



Best Answer


  • KurtKurt Member

    Sorry I know in the beginning of the attached file I have;

    "Base command line, one time with QD and another w/o"

    I meant to have;

    "Base command line, one time with MQ and another w/o"

    the logs for the runs in the body of the text do have the full command lines in them.

  • KurtKurt Member

    Ah, Thanks Geraldine. Good to know. I started to play with the LOD cut-off just to see if the distribution shifted so that somehow nothing fell below -5.

    In any case, I'll go with taking out MQ from the SNV model and wait for the RF implementation in 3.2 :)

    Thanks again,


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