I got this plot after VariantRecalibration for 42 samples in a VCF file. As it can bee seen in the plot there is no "known" variants detected. What is the problem? Which walker do you recommend to solve this issue? thanks
Could you please help me to generate the first plot in the attached file which refers to VariantRecalibrator?
In other words, is this plot generated at the same time as my_sample.bqrecal.vqsr.R.scripts.pdf? If so, maybe some R library is missing but i can't find anything wrong in the log files (my_sample.bqrecal.vqsr.R.scripts.pdf seems to me fine adn healthy).
Thanks in advance, Rodrigo.