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Integrated Genome Viewer image

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.

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    $\begingroup$ What do you see when you hover over these black lines using your mouse? Hovering on a few deletions with/without the black lines might give you an idea on the differences between them. $\endgroup$
    – Ram RS
    May 20 at 17:58
  • $\begingroup$ It doesn't show anything besides the general read metadata. Only insertions show the inserted bases on hover. Insertions with/without short black lines through them are indistinguishable on hover. $\endgroup$
    – TimD1
    May 20 at 19:39
  • $\begingroup$ Those look like some single-T reads (i.e., reads with a single base). What do you see when you hover over them? Do you get a more coherent bit of info? What does the CIGAR look like for one of those? $\endgroup$
    – Devon Ryan
    May 24 at 16:18
  • $\begingroup$ They look like short reads, but it's actually a deletion within a long read that for some reason isn't showing a black line. I'm wondering what metadata difference in the SAM/BAM could possible cause the omission of the black line... $\endgroup$
    – TimD1
    May 25 at 14:51
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Black line represents an indel. Read was lengthened to fit consensus.

No black line (blank), no read/sequence. Read likely ended or was truncated.

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  • $\begingroup$ In general, this is true. However, for my dataset, these are all long reads which I know span the region I'm looking at. For some reason, the black lines (which should be there) are not present for some INDELs. $\endgroup$
    – TimD1
    May 25 at 14:52

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