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

Bioconductor version: Release (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>

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
Video   pileup in Rsamtools


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
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
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