SV on single-end data

Question

[deniselavezzari]

Hi ! Anyone knowing a software to call structural variants on single-end data? Thanks a lot!

[dthorbur]

Do you have short or long read data?

To my knowledge there are no tools that could use just single end short reads. So much of the information used to call SVs comes from the fact you have paired reads (i.e., split and discordant reads). You could possibly use tools that create de novo assemblies and compare them to a reference, but you'd need a lot of high quality single-end data to do that. Read-depth could also be inferred from single end data, but this alone isn't that useful.

If it's long read, then there are novel tools that can call SVs with ONT or PacBio data like Sniffles.

[deniselavezzari]

Thanks a lot! I have some short reads data deriving from Ion Torrent..