CIGAR string visualization

[dlrice]

From @asifrim on November 26, 2014 16:21

It would be useful if the CIGAR string can be visualized. Specially I,D or S flags (inserstion, deletion, soft-clipping).

Insertions: IGV currently inserts a purple glyph at the position of the insertion
Deletions: IGV represents deletions by a thin black line across the bases that are deleted
Soft-clipped reads: The bases which are soft-clipped are represented as if they were SNPs (so showing the actual base in the soft-clipped segment.

In attached screenshot you can see the three types of events.

Copied from original issue: wtsi-medical-genomics/snoopy#5