An Introduction to Rsamtools
نویسنده
چکیده
The Rsamtools package provides an interface to BAM files. BAM files are produced by samtools and other software, and represent a flexible format for storing ‘short’ reads aligned to reference genomes. BAM files typically contain sequence and base qualities, and alignment coordinates and quality measures. BAM files are appealing for several reasons. The format is flexible enough to represent reads generated and aligned using diverse technologies. The files are binary so that file access is relatively efficient. BAM files can be indexed, allowing ready access to localized chromosomal regions. BAM files can be accessed remotely, provided the remote hosting site supports such access and a local index is available. This means that specific regions of remote files can be accessed without retrieving the entire (large!) file. A full description is available in the BAM format specification (http://samtools.sourceforge.net/SAM1.pdf)
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