Classification of structural variants

[ValentinaPeona]

Hello,

I have a very basic question. Given the output format of the bubble file:

gfatools bubble graph.gfa > var.bed

The output is a BED-like file. The first three columns give the position of a bubble/variation and the rest of columns are:

(4) # GFA segments in the bubble including the source and the sink of the bubble
(5) # all possible paths through the bubble (not all paths present in input samples)
(6) 1 if the bubble involves an inversion; 0 otherwise
(7) length of the shortest path (i.e. allele) through the bubble
(8) length of the longest path/allele through the bubble
(9-11) please ignore
(12) list of segments in the bubble; first for the source and last for the sink
(13) sequence of the shortest path (* if zero length)
(14) sequence of the longest path (NB: it may not be present in the input samples)

How do I get the type of SV? Is there a way to automatically classify them as insertions, deletions, inversions etc using minigraph?