How do you find the insertion, deletion and translocation?

[Chien-Yuan Chen]

There are many tools can align genome /transcriptome.
But after alignment, how do you find these lesions such insertion deletion and translocation?

[swbarnes2]

There are many tools can align genome /transcriptome.
But after alignment, how do you find these lesions such insertion deletion and translocation?

SOAP can find very small indels, of a few bases. It routinely catches single base indels on my own data.

Large deletions are pretty easy...if you have no reads covering the area, it's a large deletion. Large insertions will look like a very abrupt valley in coverage. You can also find them by de novo assembling unalignable reads.

Use paired end data. If you have many reads where one end maps to one position, and the other end maps at an unexpected distance, that's probably some kind of rearrangment.

Small deletions, like of 3 bases, are just going to be hard to find. De novo assembly can do it, if your read density is high enough.

[Chien-Yuan Chen]

Yes, we could find some lesions by pair end sequencing, but I mean the method to get all the data at a time, not by check each lesion one by one.

Some commercial sofware such as CLC genome workbench, it just only see the alignment, but it can not get the all lesions at a time!