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

Bioconductor version: Release (2.11)

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>

To install this package, start R and enter:


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
Version 1.10.2
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0 + file LICENSE
Depends methods, IRanges(>= 1.15.35), GenomicRanges(>= 1.9.48), Biostrings(>= 2.25.6)
Imports methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics(>= 0.1.3)
Suggests ShortRead(>= 1.13.19), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, RUnit
System Requirements
Depends On Me ArrayExpressHTS, BitSeq, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, girafe, leeBamViews, oneChannelGUI, qrqc, Rcade, ReQON, RNASeqDataSubset, rnaSeqMap, ShortRead, TEQC, VariantAnnotation
Imports Me annmap, ArrayExpressHTS, biovizBase, deepSNV, FunciSNP, ggbio, gmapR, HTSeqGenie, LungCancerLines, PING, R453Plus1Toolbox, rtracklayer, ShortRead, VariantAnnotation, VariantTools
Suggests Me GenomicFeatures, GenomicRanges, ind1KG, R453Plus1Toolbox, RnaSeqTutorial, seqbias, Streamer

Package Downloads

Package Source Rsamtools_1.10.2.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) Rsamtools_1.10.2.tgz
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