segment

Segmentation: Normalization of SVs into disjointed genomic regions

For SVs with a span in the genome (currently only DELs), split the overlaps into disjointed regions. This is an experimental tool that explores the possibility of assisting SV association analysis.

This tool adds an INFO field SEGCNT with holds the number of SVs overlapping the newly reported region. It also adds a FORMAT field SEG, which is the 'allele coverage' per-sample. For example, if a sample has two overlapping heterozygous deletions, the shared region will have SEG=2. If the two deletions were homozygous then SEG=4.

In the below example, the new annotations would be:

Region	INFO/SEGCNT	S1/SEG	S2/SEG	S3/SEG
A	1	2	0	0
B	2	2	1	0
C	3	2	2	2
D	2	2	1	0
E	1	0	1	0