I was hoping someone could verify how PF_INDEL_RATE is calculated in AlignmentSummaryMetrics.
The definition says: "PF_INDEL_RATE: The number of insertion and deletion events per 100 aligned bases. Uses the number of events as the numerator, not the number of inserted or deleted bases".
The code on github for calculating PF_INDEL_RATE is this:
metrics.PF_INDEL_RATE = MathUtil.divide(indels, (double) metrics.PF_ALIGNED_BASES);
I can't seem to find anywhere that suggests the rate is "per 100 aligned bases". Just want to verify that in a sample with PF_ALIGNED_BASES of 115694467, a PF_INDEL_RATE of 0.0002 would mean that there are 2 indel events in every 1000000 bases (0.0002 in 100 aligned bases), and not 23,139 indel events in 115694467 aligned bases (0.0002 * 115694467).