What does presence/absence of black lines mean in IGV? IGV (Integrated Genome Viewer) is a popular open-source tool for viewing alignment files. In my BAM file in IGV, some deletions have black lines running through them, and others don't. What causes this? Short black lines also appear adjacent to some mutations and insertions.
I generated the CIGAR for the SAM file myself, and am wondering if I made an error. I didn't find anything in IGV's documentation about this.
Black line represents an indel.  Read was lengthened to fit consensus.
No black line (blank), no read/sequence.  Read likely ended or was truncated.