As far as I know, one cannot edit (alter) alignments in IGV. Is there any tool similar to IGV that would allow looking at a small window in a bam file, manually moving some of the difficult to align reads in that region -- this is, changing the read alignments, then saving that window of the bam as another small bam file?

The only way I can think of right now is to export the bam window to multi-fasta, open it with Jalview, edit the alignments, and save to multi-fasta. Transforming back to bam is not trivial, though.

Thanks