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


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.

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.