SV Output

OSF Overview of the SV32 classification schema. The classification schema bins all SVs, apart from translocations, according to the size of the event in base pairs: 0–10kb, 10kb–100kb, 100kb–1Mb, 1Mb–10Mb, and >10Mb. Translocations, which may involve more than one chromosome, are not binned by size because they can be either balanced (where there is no net loss of genetic material on the chromosomes involved and thus the size can be described by one number) or unbalanced (where there is a net loss or gain of genetic material on the chromosomes involved and thus the sizes of the segments cannot be described by just one number). Note that whether a translocation is balanced or unbalanced is not considered in this classification schema. The different types of SVs are then further divided into clustered and non-clustered events to account for the non-random distribution of these events along the genome. Clustered events are defined as events that occur closer to each other on a chromosome than purely expected by chance.

OSF Example of SV visualization outputs once SV matrix generation is complete. A depiction of the SV32 channel counts for an individual sample. This type of visualization can be generated using SigProfilerPlotting (https://github.com/AlexandrovLab/SigProfilerPlotting) on a sample-by-sample basis, where the final output is a multi-page pdf containing plots for each sample.

OSF Example output of annotated bedpe file that classifies each SV event according to the SV32 classification scheme described above. Note the last column contains information about whether the breakpoints of an SV event were clustered or non-clustered.