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Old 01-09-2012, 11:32 AM   #1
oiiio
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Default When viewing a BAM, can you specify regions of a certain coverage?

Does anyone know of a tool to view only regions of a BAM with specific coverage? Ideally, it would constrain the coverage using either a max or min
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Old 01-09-2012, 11:39 AM   #2
swbarnes2
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You could make a pileup, which would have the depth at every point. Then some kind of script to make a .bed file of all those windows you wanted, and you can apply the .bed file to the .bam with samtools view to get a .bam just at those coordinates.

You could probably use BEDTools to do much of that. I'm not sure there's an easier way.
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Old 01-10-2012, 05:43 AM   #3
Jim Robinson
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Elaborating on this just a little... After creating the bed you can load both the bed and the BAM into IGV. Then click on the name panel over the bed track, and use ctrl-f to skip from one region to the next.
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Old 01-10-2012, 06:59 AM   #4
mgogol
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I think you could use genomeCoverageBed from bedtools for the first step. I know you could do the second part in R quite easily, but it would take me awhile to figure that one out. Once you have a bed file you could use intersectBed to get a bam just with those coords.
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