Getting coordinates with bad deep/coverage from a bam file
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5.7 years ago
Enka ▴ 10

I received .bam files for bacterial genomes sequenced by SOLiD and mapped to a reference genome by bioscope. I have found that some areas have really few reads aligned (as few as 2). I would like to know if there is a way to get the coordinates of the regions that have a deep (or coverage) below certain threeshold, so I can assess how big is this problem for each aligment.

solid bam igv resequencing • 1.4k views
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My bad. Thanks a lot.

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