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@@ -54,6 +54,10 @@ The main algorithm is based on a *priority_queue* from the standard library and
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*covtobed* relies on `libbamtools` [@bamtools] for BAM file parsing, and `cpp-optparse` [@opt] for command line option parsing.
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# Documentation
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The package documentation is maintained in the [GitHub wiki](https://github.com/telatin/covtobed/wiki). The documentation contains examples of usage, example of produced output and details about the package.
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# Example applications
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When performing target enrichment experiments (where the aim is to sequence a set of selected regions of a genome), it's important to detect a lack of coverage or insufficient coverage (*i.e.* the coverage on target is lower than `THRESHOLD`). This information can be obtained by intersecting (using *bedtools*, [@bedtools]) the BED file describing the captured target regions (usually supplied by the company producing the kit) with the output of *covtobed*.

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