To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

In most cases, you don't need to download the package archive at all.

Rsamtools

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

Bioconductor version: 3.1

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

Author: Martin Morgan, Herv\'e Pag\`es, Valerie Obenchain, Nathaniel Hayden

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Rsamtools")

PDF	R Script	An introduction to Rsamtools
PDF	R Script	Using samtools C libraries
PDF		Reference Manual
Text		NEWS
Text		LICENSE
Video		pileup in Rsamtools

Details

biocViews	Alignment, Coverage, DataImport, QualityControl, Sequencing, Software
Version	1.20.5
In Bioconductor since	BioC 2.6 (R-2.11) (5.5 years)
License	Artistic-2.0 \| file LICENSE
Depends	methods, S4Vectors(>= 0.5.11), IRanges(>= 1.99.17), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.19), XVector(>= 0.5.3), Biostrings(>= 2.33.11)
Imports	utils, BiocGenerics(>= 0.1.3), zlibbioc, bitops
LinkingTo	S4Vectors, IRanges, XVector, Biostrings
Suggests	GenomicAlignments, ShortRead(>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, RUnit, BiocStyle
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me	ArrayExpressHTS, BitSeq, chimera, CODEX, CoverageView, exomeCopy, exomePeak, GenomicAlignments, GenomicFiles, ggtut, girafe, leeBamViews, MEDIPS, methylPipe, MMDiff, oneChannelGUI, podkat, qrqc, r3Cseq, Rcade, ReQON, rfPred, RIPSeeker, rnaSeqMap, ShortRead, ssviz, systemPipeR, TBX20BamSubset, TEQC, TitanCNA, VariantAnnotation, wavClusteR
Imports Me	AllelicImbalance, annmap, ArrayExpressHTS, biovizBase, BSgenome, CAGEr, casper, CexoR, ChIPQC, cn.mops, CNVrd2, compEpiTools, CopywriteR, csaw, customProDB, derfinder, DEXSeq, diffHic, DOQTL, easyRNASeq, EDASeq, epigenomix, FourCSeq, FunciSNP, genomation, GenomicAlignments, GenomicInteractions, ggbio, GGtools, gmapR, GoogleGenomics, GreyListChIP, Gviz, gwascat, h5vc, HTSeqGenie, LungCancerLines, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, metagene, nucleR, PICS, QDNAseq, QuasR, R453Plus1Toolbox, Rariant, Repitools, RNAprobR, rtracklayer, SGSeq, similaRpeak, soGGi, SplicingGraphs, tracktables, trackViewer, TransView, VariantFiltering, VariantTools
Suggests Me	AnnotationHub, bamsignals, BaseSpaceR, BiocParallel, biomvRCNS, DiffBind, gage, GenomeInfoDb, GenomicFeatures, GenomicRanges, gQTLstats, ind1KG, metaseqR, parathyroidSE, RnaSeqTutorial, seqbias, SigFuge, Streamer
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	Rsamtools_1.20.5.tar.gz
Windows Binary	Rsamtools_1.20.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Rsamtools_1.20.5.tgz
Mac OS X 10.9 (Mavericks)	Rsamtools_1.20.5.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/Rsamtools/tree/release-3.1
Package Short Url	http://bioconductor.org/packages/Rsamtools/
Package Downloads Report	Download Stats

Documentation »

Bioconductor

Package vignettes and manuals.
Workflows for learning and use.
Course and conference material.
Videos.
Community resources and tutorials.

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Support site - for questions about Bioconductor packages
Bioc-devel mailing list - for package developers