Problem with viewing BAM files in IGV
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5 weeks ago
manfi • 0

Hi everyone, I'm quite new to bioinformatics and I'm having some beginner problems with IGV. I've got some BAM files that were generated using the GATK best practice pipeline for SNP discovery, with BAI files located in the same directory. I'm using the latest version of IGV on a Ubuntu 18.04.4 server with Java 11.

Until recently I could open my files without problems, but if I try to open them now, no data are displayed. Below I've zoomed in on a region where I know that there should be data (as verified by inspecting the BAM file with samtools view), zooming in further doesn't help. If I open a saved past session, the data are displayed with all the usual tracks, but I can't open the data which I used for this saved past session.

Any suggestions on how I can solve / troubleshoot this problem? Thanks!

enter image description here

EDIT: The solution was to select both the BAM and the BAI and to open them simultaneously.

IGV BAM • 345 views
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as verified by inspecting the BAM file with samtools view

show us a few lines of "samtools view" and show us the screenshot of IGV for one of those lines.

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Samtools view:

enter image description here

Screenshot for 1 line, it seems like the tracks aren't loaded?

enter image description here

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When one opens a BAM file in IGV, usually you can see a track name on the left. There is no track name in your IGV. BAM file was not loaded at all.

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Yes, I think this is the problem. I can't load any BAM files and when I click on them in "Load from File" nothing happens (no error messages either).

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try to install a fresh copy of IGV maybe. I faced such problems and usually I solve them with magical dances. It is more of an IT problem, sadly. try drag-n-drop bam files, try to load some other tracks (bed files for example).

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I've found the solution: I had to select the bam AND the bai using ctrl when opening, then it suddenly loads the way it should (I thought the bai was always opened automatically?)

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Magic! Indeed, it needs BAI =) glad you've solved it

I don't load BAI files indeed, but they need to have the same name and be located in the same folder

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5 weeks ago

those reads have the following flags:

1153: read is PCR or optical duplicate (0x400) 2161: supplementary alignment (0x800)

or a very low MAPQ 4,4,1,2

if you really want to see those reads, update the preferences in IGV. "Filter duplicate reads, Filter supplementary alignments , Mapping quality threshold" http://software.broadinstitute.org/software/igv/Preferences

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