I'm looking for a aligner or read mapper that could handle larger indels well, up to 200bp out of 300~500bp reads. These reads are merged paired-end reads from Illumina MiSeq platform. BWA MEM seems to be working well all the way to ~60bp indels, but would just do clipping for events larger than that.I have tried minimap2 using the "map-ont" mode (aided by "--lj-min-ratio=0.2" option), pretending those are nanopore amplicon reads, and got mixed results. The "splice" mode would give me good results for deletions but for large insertions, especially those approaching 100bp, it has been hit or miss. Of course, there is the other path of running some kind of assembly process and skip the mapping, but that is a complete different ball game and opens a can of worms. Would anyone have some advices on this?
