Exporting Coverage Track

[viv]

Hi, I was wondering if there was any way to download or export the coverage .bam file. I'm looking to get the total count at each base pair. The information is available when I scroll over the coverage track but I want to export the track so I can get that information for the entire sequence and in a file format. Thanks.

[Helga Thorvaldsdottir]

You can use the igvtools "count" tool to create a coverage file.
igvtools can be used from the IGV desktop application, or run from the
command line. See the documentation here:
https://www.broadinstitute.org/igv/igvtools, and follow the links at the
bottom of the page for more information about usage.

Helga

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