Introduction

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. 

How to view soft-clipping in IGB

Note: Soft-clipped sections of reads are not visible in versions of IGB prior to 9.1

To view soft-clipping within IGB, first load a BAM file:

1. Open BAM file.
2. Zoom in on the gene or region of interest.
3. Click Load Data.

Soft-clipping is enabled by default in IGB, with the soft-clipped section of the read displayed in gray.

To configure the appearance of soft-clips:

1. Right-click the reads track label.
2. Select Configure soft-clip.

Options for viewing soft-clipping include:

1. Show as default color - Soft-clipping shows as a default gray.
2. Show as custom color... - Using a color picker, soft-clipping shows as selected color.
3. Show as bases - Soft-clipping shows as Residue Colors.
4. Hide soft-clipping - Soft-clipping is hidden.

Track Operations and Soft-clipping

Track Operations behave differently when soft-clipping is present.

• Depth Graph (All) and Depth Graph (Start) ignore the soft-clipped parts of reads.
• Mismatch Graph and Mismatch Pileup Graph include the soft-clipped parts of reads.