Soft-Clipped reads

[Zona Lin]

Hi!

I'm dealing with a highly repeat region and got some question wish someone can help!

I compared the two figures, with/without turn on 'view soft-clipped reads',

I found that the coverage track is the same (read depth will drop intensely in the middle), but the alignment track show so much more reads with 'view soft-clipped reads' on than without the 'view soft-clipped reads' function.

So there are reads won't show up without turn on 'view soft-clipped reads' (might because contain too many soft-clipped bases?).

I would like to know:

1. What is the criteria that IGV tools decide not to show reads when without 'view soft-clipped reads'. Is it depends on the amount of soft-clipped reads? Or specific flags? 

2. Does the read depth (coverage track) include soft-clipped reads/bases? And is there a way that can show total reads depth when 'view soft-clipped reads' is on?

Thank you sooo much!

[igv-help]

If a read has any soft-clipped bases, it is specified in the read's CIGAR string in the BAM file, as described in the file format  specification: https://samtools.github.io/hts-specs/SAMv1.pdf. If the IGV preference "Show soft-clipped bases" is enabled, those bases will be displayed. For the coverage track, all soft-clipped bases are ignored. So the coverage track is always the same, whether or not the soft-clipped bases are displayed. There is no option/preference to change this behavior.