I am trying to use the NGSrich tool to compute and visualise enrichment of target regions in an exome-sequencing experiment.
The tool seems to produce some useful output to hand to my collaborators, but I am not clear on the metrics reported in the HTML file. Does anyone have any detailed explanation of these metrics? Specifically,
The #target regions metric seems to differ if I gave the same target regions file, but different bam files
Do the Coverage metrics refer to On-target reads only? And on a per-base or per-Amplicon basis? What exactly are the percentage reported?