cuteSV calling in wrong position

[Akazhiel]

Hello!

I'm working with corrected long reads and found something odd when working with cuteSV on this data. And that is the fact that when you check some SVs in IGV you can clearly see the breakpoints, but for some reason cuteSV marks them in different positions.

In this first image you can see how all the insertions fall in the same position but both cuteSV and Sniffles predict the position erroneously.

The same seems to happen in this one, although this one is not as clean as the previous one.

I've seen it happen with other types of SVs where the breakpoint differs in 1-2bp from the actual one, although I can't provide images of those ones as of now.

What could be causing this behaviour?

Thanks in advance.

[tjiangHIT]

Hello @Akazhiel,

Thank you for your valuable question. Your confusion is similar to another issue about #65 approximately. A new modification of the breakpoint has been updated. Please git clone the latest codes to check it. BTW, a new version on Bioconda and PyPi will be pushed when all known bugs have been fixed. Thank you.

Tao