inversion detection using raw reads

[sadiexiaoyu]

Hi, All,

I would like to use the raw genome pair-end data or the assembled scaffold and RAD sequencing data to detect inversion and the breaking point for special region in the genome and special chromosome. I heard that using pair-end data can deal with these questions, but I do not have much experience on it... Could anyone give me any suggestion?



Thanks in advance!


All the best,

Sadiexiaoyu

[BnaT]

There's a wide variety of SV callers that support inversion calling. I'd suggest DELLY or Pindel, they do well with inversions and are simple to use.

[SNPsaurus]

RAD will be too dispersed to reliably detect a breakpoint. RAD genetic maps would do that, however.