Structural variants for cell line SA921

Structural variant breakpoints called by destruct on the OV2295-derived cell line SA921, one of the samples in CNbins, so the two can be plotted together.

SVs

Format

A data frame with 447 rows and 9 columns:

chromosome_1, position_1, strand_1

first breakend

chromosome_2, position_2, strand_2

second breakend

type

deletion, duplication, inversion or translocation

rearrangement_type

destruct's finer label, including foldback and balanced

read_count

number of supporting reads (destruct num_reads)

Source

destruct breakpoint calls for SA921, from the OV2295 single cell whole genome sequencing dataset.

Details

Filtered to calls supported by at least 5 reads. destruct's own filters (is_filtered, is_germline, is_dgv) were already applied upstream; the read-support floor removes the long tail of low-confidence calls, most of which are spurious foldbacks.

This is the column format plotCNprofile() expects for its SV argument. strand_1 and strand_2 must be "+"/"-", and read_count is required by the "lines_and_arcs" style.

See also

plotCNprofile() for plotting these alongside copy number, and the "Structural variant visualization" vignette.