Visualization tools for split read / structural variants

Visualization tools for split read / structural variants

0

Hi everyone,

I have been trying to curate my SV call set by visually going through the bamsnap images (a static version of IGV) of each SV region. However, it is difficult to look at long-range information, such as the paired-end reads, or when a read is mapped to different regions, using this approach.

I am wondering if there exist tools that can: 1) show all the alignment with respect to the reference; 2) show the mapping of the split reads to reference; 3) extract pairs of discordant/clipped reads (not necessarily have to be the same tool).

I would also love to know how other people are curating SV call sets. Any advice would be greatly appreciated.


variant


structural


split


visualization


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