...
Soft-clipping of reads is done during alignment to mask portions of the reads that do not align to the reference sequence.
Visualizing soft-clipping can be useful for identifying contaminating adapter sequences or detecting structural variants.
...
Note: When using the hide soft-clipping option, a line showing the full length of the read including the soft-clipped portion will appear.
To completely hide the soft-clipping portion of the read, use the Show as Custom Color soft-clip option, and select the same color as the background for the track.
...