fgsv should enable easier review in IGV

[tfenne]

fgsv generates an output BAM from the pileup phase that has tags like:

be:Z:0;left;from;read_pair
be:Z:0;left;into;read_pair
be:Z:0;left;from;split_read
be:Z:0;left;into;split_read
be:Z:0;right;from;split_read
be:Z:0;right;into;split_read

where records from the same template (or same read in the case of split reads) get different values. This makes it really hard to group/color/etc. in IGV and see all read alignments that support a given breakpoint.

I would suggest that some of this information should be extracted into individual tags. At least the breakpoint ID, and possibly also the left/right into a second tag. That way users could group by breakpoint ID and get a view of all the reads supporting the break point together.

[nh13]

@tfenne here's a little tool that may help for now: https://gist.github.com/nh13/79609e2f9d638e98e4db1a1b4a949b5e