software to estimate pair-end reads distance

[Pol8]

Dear all,

is there a way to estimate if the distance among pair-end reads is higher or lower than expected, compared to the reference (and so, that there are deletions/insertions in the pair-end reads)? And to calculate how many read pairs fall in each category?

[Brian Bushnell]

ALE does something like this. Though if you have long enough reads, mapping and calling variants should be much more accurate for indel detection than inferring based on insert size. BBMap, specifically, is very good at accurately mapping reads containing large indels.