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This is the development version of BadRegionFinder; for the stable release version, see BadRegionFinder.

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Bioconductor version: Development (3.19)

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

Author: Sarah Sandmann

Maintainer: Sarah Sandmann <sarah.sandmann at>

Citation (from within R, enter citation("BadRegionFinder")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews Alignment, Classification, Coverage, Sequencing, Software, WholeGenome
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License LGPL-3
Imports VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics
System Requirements
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Suggests BSgenome.Hsapiens.UCSC.hg19
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Follow Installation instructions to use this package in your R session.

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