Hey all,

Currently I'm doing battle with some ONT Long-Read WGS data, and trying to get my feet wet with Structural Variation analysis. Right now I want to extract reads from my alignment that support a breakpoint's existence, since the usual tools have not produced satisfactory results.

My question is: if you were to fish for reads that span a chromosomal breakpoint, would you use reads that have supplementary alignments (i.e., the SA tag), or reads that have been softclipped a considerable amount, or both? I'm taking into consideration all of these subsets, but wanted to hear from the community if there is some established way to do this.