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

Bioconductor version: 2.13

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>

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


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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 1.14.3
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0 | file LICENSE
Depends methods, IRanges(>= 1.19.11), GenomicRanges(>= 1.13.35), XVector, Biostrings(>= 2.29.7)
Imports utils, BiocGenerics(>= 0.1.3), zlibbioc, bitops
Suggests 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
Depends On Me ArrayExpressHTS, BitSeq, casper, chimera, CNVrd2, deepSNV, easyRNASeq, EDASeq, exomeCopy, exomePeak, GGtools, ggtut, girafe, leeBamViews, MMDiff, oneChannelGUI, prebs, qrqc, r3Cseq, Rcade, ReQON, rfPred, RIPSeeker, rnaSeqMap, ShortRead, TBX20BamSubset, TEQC, VariantAnnotation
Imports Me AllelicImbalance, annmap, ArrayExpressHTS, biovizBase, CAGEr, CexoR, cn.mops, customProDB, deepSNV, DEXSeq, DNaseR, FunciSNP, ggbio, gmapR, Gviz, HTSeqGenie, LungCancerLines, MEDIPS, PICS, QuasR, R453Plus1Toolbox, Repitools, rtracklayer, TransView, VariantAnnotation, VariantTools
Suggests Me AnnotationHub, biomvRCNS, DiffBind, gage, GenomicFeatures, GenomicRanges, ind1KG, parathyroidSE, QuasR, R453Plus1Toolbox, RNAseqData.HNRNPC.bam.chr14, RnaSeqTutorial, seqbias, SigFuge, SplicingGraphs, Streamer

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Package Source Rsamtools_1.14.3.tar.gz
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Mac OS X 10.6 (Snow Leopard) Rsamtools_1.14.3.tgz
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