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Old 06-27-2011, 04:59 PM   #1
cswarth
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Location: seattle

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Default missing reads in IGV display

Hello all,

When displaying a BAM file in IGV (1.5.52) I noticed that the coverage track reflects the correct number of reads at a locus but the pileup display below only shows a fraction of the reads. I checked View->Preferences->Alignments and made sure that it was not filtering duplicate reads and not restricting based on quality.

At one locus the coverage track tells me (correctly) that I have 19 reads, but the pileup display below only shows 10 of them. Another locus has 211000 reads but the pileup shows maybe a couple hundred.

Is there any way I can control how many reads IGV to displays? I understand it would be difficult for it to display 200K reads at one locus, but it should be able to display 19 of them.

Thanks in advance for any help.
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Old 06-27-2011, 07:17 PM   #2
Kennels
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I'm not sure if this would apply to your case, but I've had memory limitations with earlier versions of IGV leading to incomplete .bam file loading/refreshing/display of reads, especially if i try zooming in and out. IGV2.0 is out if you want to check if it is a memory issue. It resolved the issue for me.
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Old 06-28-2011, 08:30 AM   #3
cswarth
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Thanks, upgrading to IGV 2.0 seems to have fixed the problem.
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