SV breakpoints -- are they grouped? How are they determined?

Structural Variation
1

Hello!

Are SV variants with multiple similar (close by) breakpoints grouped together into one variant? If so, how are the breakpoints determined?

For example, DEL_CHR15_942499A6 with explicit breakpoints of 15:43602626-43710198 was seen in 1378 alleles. Were these exact breakpoints occurring for each allele? Publications have indicated that deletions are frequent in this highly homologous region, as it includes a four gene tandem duplication, and have varied breakpoints.

2

Hey! we merged SV breakpoints across samples in the pipeline; for large CNVs (>5Kb), we required 80% reciprocal overlap for variants to be merged; for other variants that relied on aberrant pair-ends and split read evidences, we required 10% reciprocal overlap and 300bp max breakpoint distances for them to be merged; the median base would be assigned as breakpoints for each cluster.