IGV - is it possible to adjust bases horizontally for misalignment

Question

[Xinxin]

I am working on a set of aligned reads and I believe 10% of them were misaligned; for example:

CCAGGGGATC

-2-CCAGGAGATTC ("-2-" means IGV believes that there are 2 deletions and moved that read to the right for 2 positions.)

I want to move the second reads to the left for 2 positions, so it can be looked like:

CCAGGGGATC

CCAGGAGATTC

Can I do that in IGV? I am using IGV to check for misalignment but I cannot drag those misaligned reads over horizontally.

[GenoMax]

I don't think any genome browsers allow editing of alignments. They are simply "browsers". These alignments would need to be changed in BAM file itself which would mean changing CIGAR strings and other things. Not simple to do via a GUI.

Answer 1

[colindaven]

You can use a tool like abra2 on github to do realignment. Results may vary, and it is computationally expensive.

https://github.com/mozack/abra2

[GenoMax]

This question is about doing a specific edit in a browser. So while this tool is great it does not help with this specific request.

[colindaven]

True, but the question actually wants a solution, so with both answers combined then that solution might be attainable.