Interpreting MultiQC plot of GATK BaseRecalibration data?
Turns out two recalibration tables are needed to show pre-recalibration and post-recalibration plots. I previously only had generated the pre-calibration table by running BaseRecalibrator on the BAM that hadn't undergone ApplyBQSR to adjust base scores. Here are the steps to show pre and post recalibration plots in MultiQC:


Run BaseRecalibrator on your initial input BAM. This will create a recalibration table with the original base scores. 
Run ApplyBQSR with the recalibration table from step 1 to create a new BAM with the adjusted base quality scores.
Run BaseRecalibrator on the adjusted BAM generated in step 2 to create a new recalibration table with the adjusted base quality scores. 
Use both recalibration tables as inputs to MultiQC. This should create both plots.