Investigating paired-end read orientations in nested inversions
For paired-end Illumina reads, the normal read orientation is +/- (forward-reverse).
When reads span an inversion breakpoint, the orientation changes to ++ or --.
However, when inversions overlap, a breakpoint may be inside another inversion. Each overlapping inversion flips the expected signature:
0, 2, 4... overlapping inversions: ++/-- (standard inversion
signature)
1, 3, 5... overlapping inversions: +/- (appears normal!)
This tool calculates the expected read orientation signature at each breakpoint, accounting for nested inversions.