Genomic inversions are not aligned.

[mnshgl0110]

Hi.

It seems that after the recent updates (v2.18+) minimap2 is not able to align inverted regions between genomes correctly. I simulated inversions ranging from 10bp to 50kpb (SIZES = [10, 50, 100, 500, 1000, 2000, 5000, 10000, 50000]) in a 1Mbp long sequence and aligned the sequences using minimap2 v2.17 and v2.22.

Both version missed 10, 50, 100 bp long inversions. Version2.17 identified all inversions >=500bp long correctly. However, Version2.22 could not identify 10Kbp and 50Kbp inversions.

The alignments from the new version disallow proper variant calling, therefore I would like to have the same sensitivity as v2.17. Is it possible to update minimap2 to get the same sensitivity as v2.17? What other options are there to ensure that inverted regions are correctly aligned?

[lh3]

Duplicated. See #816. Resolved on the github HEAD.