I'm using GATK4 to build a somatic variant calling pipeline. The pipeline uses MultiQC to aggregate quality control data, and one of the QC measures reported is base quality score recalibration from GATK4's
BaseRecalibraton. The description in MultiQC says
This plot shows the distribution of base quality scores in each sample before and after base quality score recalibration (BQSR). Applying BQSR should broaden the distribution of base quality scores.
The black line is for my tumor sample and blue line is my normal sample. I don't understand how the before and after distributions are both shown in the plot as I only see 1 distribution per sample. Am I missing something, or should there be a "Post-calibration Count" plot that isn't shown? If nothing is missing, how should I be interpreting the plot?