Recently, we performed exome sequencing for 3 samples using Nextera sequencing machine. We used new kit for exome sequencing. So I am interested in finding out the on-target and off-target percentage of reads from my exome sequencing run.
This is my understanding, On-target - Reads that are aligned to the regions that are targeted (exome regions as per the manifest file). Off-target - Reads that are aligned to the regions which are not targeted.
What should be the percentage of reads covering on-target region? and How can we calculate the on-target reads from BAM file? Which tool is useful in getting the percentage of reads covering on-target and off-target regions?