Binary alignment (BAM), variant call (BCF), or tabix file import

Bioconductor version: 2.10

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Author: Martin Morgan, Herv\'e Pag\`es

Maintainer: Bioconductor Package Maintainer <maintainer at>

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To cite this package in a publication, start R and enter:



PDF R Script An introduction to Rsamtools
PDF R Script Using samtools C libraries
PDF   Reference Manual
Text   NEWS


biocViews DataImport, HighThroughputSequencing, Sequencing, Software
Depends methods, IRanges(>= 1.13.30), GenomicRanges(>= 1.7.43), Biostrings(>= 2.21.12)
Imports methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics(>= 0.1.3)
Suggests ShortRead(>= 1.13.19), GenomicFeatures, RUnit, KEGG.db
System Requirements
License Artistic-2.0 + file LICENSE
Depends On Me ArrayExpressHTS, BitSeq, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, girafe, ind1KG, leeBamViews, oneChannelGUI, qrqc, ReQON, rnaSeqMap, ShortRead, TEQC, VariantAnnotation
Imports Me ArrayExpressHTS, biovizBase, deepSNV, ggbio, R453Plus1Toolbox, rtracklayer, ShortRead, VariantAnnotation
Suggests Me GenomicRanges, R453Plus1Toolbox, RnaSeqTutorial, seqbias, Streamer
Version 1.8.6
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source Rsamtools_1.8.6.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary Rsamtools_1.8.6.tgz
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