How to call small SVs (<50bp) from single end reads?

Question

[jseg]

Hi all,

I'm looking for a way to efficiently call small structural variants (<50bp) using single-end reads (inputs from ChIP-seq). The methods I found require paired-end reads, so do you know any efficient approach that uses single-end reads?

Regards.

[lieven.sterck]

I might be wrong here, but SV is hard (impossible) to detect with SE reads, mainly because aligning the reads with such mismatch/gap will be nearly impossible.