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Old 08-07-2015, 07:00 AM   #1
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Location: Texas

Join Date: Aug 2015
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Default How to view BAM files in IGV?

I am trying to view a BAM file with IGV version 2.3 launched with 1.2 GB. I load the BAM file, which is about 650 MB, but the screens in IGV are completely blank. IGV opens as a separate application in Java.

I attached a screenshot.

Thanks for any help.
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Old 08-07-2015, 07:09 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077

Do you have the corresponding index file (with extension .bai) available in the same folder as your bam file?

By default IGV opens in a "zoomed-out" mode. You have to select a chromosome and then keep zooming in before you will see data show up in the view pane.
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