To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

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

Rsamtools

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

Bioconductor version: 2.14

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, Valerie Obenchain

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

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

Installation

To install this package, start R and enter:

source("http://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

Details

biocViews	DataImport, Sequencing, Software
Version	1.16.1
In Bioconductor since	BioC 2.6 (R-2.11)
License	Artistic-2.0 \| file LICENSE
Depends	methods, IRanges(>= 1.21.10), GenomicRanges(>= 1.15.11), XVector(>= 0.3.2), Biostrings(>= 2.31.3), GenomeInfoDb(>= 0.99.17)
Imports	utils, BiocGenerics(>= 0.1.3), zlibbioc, bitops
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
System Requirements
URL	http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me	ArrayExpressHTS, BitSeq, chimera, CNVrd2, CoverageView, deepSNV, EDASeq, exomeCopy, exomePeak, GenomicAlignments, GenomicFiles, ggtut, girafe, leeBamViews, MMDiff, oneChannelGUI, qrqc, r3Cseq, Rcade, ReQON, rfPred, RIPSeeker, rnaSeqMap, ShortRead, TBX20BamSubset, TEQC, VariantAnnotation
Imports Me	AllelicImbalance, annmap, ArrayExpressHTS, biovizBase, BSgenome, CAGEr, casper, CexoR, ChIPQC, cn.mops, customProDB, deepSNV, DEXSeq, DNaseR, easyRNASeq, FunciSNP, GenomicAlignments, ggbio, GGtools, gmapR, Gviz, gwascat, h5vc, HTSeqGenie, LungCancerLines, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MEDIPS, PICS, QDNAseq, QuasR, R453Plus1Toolbox, Rariant, Repitools, rtracklayer, trackViewer, TransView, VariantFiltering, VariantTools
Suggests Me	AnnotationHub, BaseSpaceR, biomvRCNS, DESeq2, DiffBind, gage, GenomicFeatures, GenomicRanges, ind1KG, metaseqR, parathyroidSE, QuasR, RnaSeqTutorial, seqbias, SigFuge, SplicingGraphs, Streamer

Package Archives

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

Package Source	Rsamtools_1.16.1.tar.gz
Windows Binary	Rsamtools_1.16.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Rsamtools_1.16.1.tgz
Mac OS X 10.9 (Mavericks)	Rsamtools_1.16.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Oligonucleotide Arrays
High-throughput Sequencing
Counting Reads for Differential Expression (parathyroideSE vignette)
Annotation
Annotating Variants
Annotating Ranges
Flow Cytometry and other assays
Candidate Binding Sites for Known Transcription Factors
Cloud-enabled cis-eQTL search and annotation

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