edit read alignments in bam region

Question

[14134125465346445]

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

[Devon Ryan]

Have you tried just using GATK with its IndelRealigner? You might give that a go before attempting the manual route.

[14134125465346445]

In this particular case, the aim is to manually edit small windows of a bam file.

[Ashutosh Pandey]

Well you can also choose a small window for realignment using GATK IndelRealigner but you won't be able to align reads manually.