Bug in VariantRecalibrator
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.