Precomputing Coverage with igvtools

Last updated on 2026-09-03 | Edit this page

Overview

Questions

  • Why does my coverage track go blank when I zoom out?
  • How do I precompute coverage data so it is visible at any zoom level?

Objectives

  • Explain why coverage disappears when zooming out on a large BAM file.
  • Use igvtools to precompute a coverage summary (TDF) file.
  • Associate a precomputed coverage file with an alignment track.

This episode assumes you already have loaded, from the previous episodes:

  • the reference genome chr1.fasta, and
  • the alignment file igvData/snps/NA12878.SLX.sample.bam.

The problem: no coverage at low zoom levels

Zoom all the way out by clicking the leftmost tick on the “railroad track” zoom widget. Notice that the coverage track for NA12878.SLX.sample.bam now shows no data at all, just a message like “Zoom in to see coverage.”

Zoomed-out view showing no coverage data, and the igvtools Run dialog
No coverage is shown at low zoom levels until it has been precomputed.

By default, IGV computes coverage on the fly from the reads currently visible in a BAM file. At low zoom levels this would mean scanning huge numbers of reads just to draw a rough summary, so IGV instead only computes coverage once you are zoomed in far enough that this is fast. To see accurate coverage at any zoom level, you need to precompute it once, ahead of time, using the igvtools Count function.

Precompute coverage with igvtools

Select Tools > Run igvtools…, then in the dialog:

  1. Select Count from the Command drop-down menu.
  2. Set the Input File to NA12878.SLX.sample.bam in igvData/snps/. The Output File will automatically be set to the same folder and file name, with a .tdf suffix added.
  3. Keep the defaults for all other values, and click Run.

Wait until the Messages area shows “Done”, then click Close.

Associate the TDF file with the coverage track

Right-click (Mac: control-click) anywhere on the coverage track for NA12878.SLX.sample.bam in the IGV window, and select Load pre-computed coverage data…. Browse to igvData/snps/ and select the new NA12878.SLX.sample.bam.tdf file.

Loading precomputed coverage data and the resulting coverage spikes
Associating the newly created TDF file with the coverage track, revealing three spikes of coverage.

You should now see three spikes of coverage across the whole chromosome. This sample BAM file was deliberately stripped down for the workshop and only contains reads in these three regions — the leftmost spike corresponds to the snp1 locus from the previous episode.

Challenge

Zoom back in

Zoom in on the leftmost coverage spike until you reach base-pair resolution. What locus do you land on?

Zooming into the leftmost spike brings you back to the snp1 locus explored in Viewing Alignments and SNPs — the precomputed coverage track and the on-the-fly coverage you saw there are showing the same underlying reads, just computed differently depending on zoom level.

Key Points
  • IGV computes BAM coverage on the fly at high zoom levels, but does not attempt this at low zoom levels for performance reasons.
  • Use Tools > Run igvtools… > Count to precompute a .tdf coverage summary file for a BAM file.
  • Attach a precomputed .tdf file to a coverage track via right-click > Load pre-computed coverage data….