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

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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
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0 | file LICENSE
Version
1.26.1
URLs

View on Bioconductor

Man pages

applyPileups
Apply a user-provided function to calculate pile-up...
ApplyPileupsParam-class
Parameters for creating pileups from BAM files
BamFile-class
Maintain and use BAM files
BamViews-class
Views into a set of BAM files
BcfFile-class
Manipulate BCF files.
defunct
Rsamtools Deprecated and Defunct
deprecated
Deprecated functions
FaFile-class
Manipulate indexed fasta files.
headerTabix
Retrieve sequence names defined in a tabix file.
indexTabix
Compress and index tabix-compatible files.
pileup
Use filters and output formats to calculate pile-up...
PileupFiles-class
Represent BAM files for pileup summaries.
quickBamFlagSummary
Group the records of a BAM file based on their flag bits and...
readPileup
Import samtools 'pileup' files.
RsamtoolsFile-class
A base class for managing file references in Rsamtools
RsamtoolsFileList-class
A base class for managing lists of Rsamtools file references
Rsamtools-package
'samtools' aligned sequence utilities interface
scanBam
Import, count, index, filter, sort, and merge 'BAM' (binary...
ScanBamParam-class
Parameters for scanning BAM files
scanBcf
Operations on 'BCF' files.
ScanBcfParam-class
Parameters for scanning BCF files
scanFa
Operations on indexed 'fasta' files.
scanTabix
Operations on 'tabix' (indexed, tab-delimited) files.
seqnamesTabix
Retrieve sequence names defined in a tabix file.
TabixFile-class
Manipulate tabix indexed tab-delimited files.
testPairedEndBam
Quickly test if a BAM file has paired end reads
zip
File compression for tabix (bgzip) and fasta (razip) files.

Files in this package

Rsamtools/DESCRIPTION
Rsamtools/LICENSE
Rsamtools/NAMESPACE
Rsamtools/NEWS
Rsamtools/R
Rsamtools/R/AllClasses.R
Rsamtools/R/AllGenerics.R
Rsamtools/R/asBam.R
Rsamtools/R/countBam.R
Rsamtools/R/filterBam.R
Rsamtools/R/idxstatsBam.R
Rsamtools/R/indexBam.R
Rsamtools/R/io_bam.R
Rsamtools/R/mergeBam.R
Rsamtools/R/methods-ApplyPileupsParam.R
Rsamtools/R/methods-BamFile.R
Rsamtools/R/methods-BamFileList.R
Rsamtools/R/methods-BamSampler.R
Rsamtools/R/methods-BamViews.R
Rsamtools/R/methods-BcfFile.R
Rsamtools/R/methods-FaFile.R
Rsamtools/R/methods-PileupFiles.R
Rsamtools/R/methods-RsamtoolsFile.R
Rsamtools/R/methods-RsamtoolsFileList.R
Rsamtools/R/methods-ScanBVcfParam.R
Rsamtools/R/methods-ScanBamParam.R
Rsamtools/R/methods-TabixFile.R
Rsamtools/R/phred2ASCIIOffset.R
Rsamtools/R/pileup.R
Rsamtools/R/pkgconfig.R
Rsamtools/R/quickBamFlagSummary.R
Rsamtools/R/readPileup.R
Rsamtools/R/scanBam.R
Rsamtools/R/scanBamHeader.R
Rsamtools/R/scanBcf.R
Rsamtools/R/scanBcfHeader.R
Rsamtools/R/sortBam.R
Rsamtools/R/testPairedEndBam.R
Rsamtools/R/utilities.R
Rsamtools/R/zip_compression.R
Rsamtools/R/zzz.R
Rsamtools/Rsamtools.mk.win
Rsamtools/build
Rsamtools/build/vignette.rds
Rsamtools/inst
Rsamtools/inst/doc
Rsamtools/inst/doc/Rsamtools-Overview.R
Rsamtools/inst/doc/Rsamtools-Overview.Rnw
Rsamtools/inst/doc/Rsamtools-Overview.pdf
Rsamtools/inst/doc/Rsamtools-UsingCLibraries.R
Rsamtools/inst/doc/Rsamtools-UsingCLibraries.Rnw
Rsamtools/inst/doc/Rsamtools-UsingCLibraries.pdf
Rsamtools/inst/extdata
Rsamtools/inst/extdata/ce2dict1.fa
Rsamtools/inst/extdata/ce2dict1.fa.fai
Rsamtools/inst/extdata/ex1.bam
Rsamtools/inst/extdata/ex1.bam.bai
Rsamtools/inst/extdata/ex1.bcf
Rsamtools/inst/extdata/ex1.bcf.bci
Rsamtools/inst/extdata/ex1.sam
Rsamtools/inst/extdata/example.gtf.gz
Rsamtools/inst/extdata/example.gtf.gz.tbi
Rsamtools/inst/extdata/example_from_SAM_Spec.bam
Rsamtools/inst/extdata/example_from_SAM_Spec.bam.bai
Rsamtools/inst/extdata/example_from_SAM_Spec.sam
Rsamtools/inst/extdata/no_which_buffered_pileup.bam
Rsamtools/inst/extdata/no_which_buffered_pileup.bam.bai
Rsamtools/inst/extdata/no_which_buffered_pileup.sam
Rsamtools/inst/extdata/no_which_whole_file.bam
Rsamtools/inst/extdata/no_which_whole_file.bam.bai
Rsamtools/inst/extdata/no_which_whole_file.sam
Rsamtools/inst/extdata/olaps.Rda
Rsamtools/inst/extdata/pileup.txt
Rsamtools/inst/extdata/querybins.bam
Rsamtools/inst/extdata/querybins.bam.bai
Rsamtools/inst/extdata/querybins.sam
Rsamtools/inst/extdata/revbins.bam
Rsamtools/inst/extdata/revbins.bam.bai
Rsamtools/inst/extdata/revbins.sam
Rsamtools/inst/extdata/samtools-github.txt
Rsamtools/inst/extdata/slxMaq09_urls.txt
Rsamtools/inst/extdata/tagfilter.bam
Rsamtools/inst/extdata/tagfilter.bam.bai
Rsamtools/inst/extdata/tagfilter.sam
Rsamtools/inst/extdata/tiny.bam
Rsamtools/inst/extdata/tiny.bam.bai
Rsamtools/inst/extdata/tiny.sam
Rsamtools/inst/extdata/tophat
Rsamtools/inst/extdata/tophat/README
Rsamtools/inst/extdata/tophat/accepted_hits.sam
Rsamtools/inst/extdata/tophat/coverage.wig
Rsamtools/inst/extdata/tophat/junctions.bed
Rsamtools/inst/scripts
Rsamtools/inst/scripts/BamViews-1000g.R
Rsamtools/inst/scripts/features.R
Rsamtools/inst/scripts/remote_test.R
Rsamtools/inst/scripts/update-samtools.sh
Rsamtools/inst/unitTests
Rsamtools/inst/unitTests/cases
Rsamtools/inst/unitTests/cases/ex1.sam.gz
Rsamtools/inst/unitTests/cases/ex1_noindex.bam
Rsamtools/inst/unitTests/cases/ex1_shuf1000.bam
Rsamtools/inst/unitTests/cases/ex1_shuf1000.bam.bai
Rsamtools/inst/unitTests/cases/ex1_unsort.bam
Rsamtools/inst/unitTests/cases/ex1_zero_index.bam.bai
Rsamtools/inst/unitTests/cases/no_SAMPLE_header.vcf
Rsamtools/inst/unitTests/cases/no_header_line.vcf
Rsamtools/inst/unitTests/cases/pileup-no-stars.txt
Rsamtools/inst/unitTests/cases/plp_refskip.bam
Rsamtools/inst/unitTests/cases/plp_refskip.bam.bai
Rsamtools/inst/unitTests/test_BamFile.R
Rsamtools/inst/unitTests/test_BamViews.R
Rsamtools/inst/unitTests/test_BcfFile.R
Rsamtools/inst/unitTests/test_FaFile.R
Rsamtools/inst/unitTests/test_RsamtoolsFile.R
Rsamtools/inst/unitTests/test_TabixFile.R
Rsamtools/inst/unitTests/test_applyPileups.R
Rsamtools/inst/unitTests/test_asBam.R
Rsamtools/inst/unitTests/test_bam.R
Rsamtools/inst/unitTests/test_bam_count.R
Rsamtools/inst/unitTests/test_bam_header.R
Rsamtools/inst/unitTests/test_compression.R
Rsamtools/inst/unitTests/test_mapqfilter.R
Rsamtools/inst/unitTests/test_phred2ASCIIOffset.R
Rsamtools/inst/unitTests/test_pileup_nowhich.R
Rsamtools/inst/unitTests/test_pileup_querybins.R
Rsamtools/inst/unitTests/test_pileup_revbins.R
Rsamtools/inst/unitTests/test_pileup_single_range.R
Rsamtools/inst/unitTests/test_readPileup.R
Rsamtools/inst/unitTests/test_scanBamFlag.R
Rsamtools/inst/unitTests/test_sortBam_test.R
Rsamtools/inst/unitTests/test_tagfilter.R
Rsamtools/inst/unitTests/test_testPairedEndBam.R
Rsamtools/inst/unitTests/test_utilities.R
Rsamtools/man
Rsamtools/man/ApplyPileupsParam-class.Rd
Rsamtools/man/BamFile-class.Rd
Rsamtools/man/BamViews-class.Rd
Rsamtools/man/BcfFile-class.Rd
Rsamtools/man/FaFile-class.Rd
Rsamtools/man/PileupFiles-class.Rd
Rsamtools/man/Rsamtools-package.Rd
Rsamtools/man/RsamtoolsFile-class.Rd
Rsamtools/man/RsamtoolsFileList-class.Rd
Rsamtools/man/ScanBamParam-class.Rd
Rsamtools/man/ScanBcfParam-class.Rd
Rsamtools/man/TabixFile-class.Rd
Rsamtools/man/applyPileups.Rd
Rsamtools/man/defunct.Rd
Rsamtools/man/deprecated.Rd
Rsamtools/man/headerTabix.Rd
Rsamtools/man/indexTabix.Rd
Rsamtools/man/pileup.Rd
Rsamtools/man/quickBamFlagSummary.Rd
Rsamtools/man/readPileup.Rd
Rsamtools/man/scanBam.Rd
Rsamtools/man/scanBcf.Rd
Rsamtools/man/scanFa.Rd
Rsamtools/man/scanTabix.Rd
Rsamtools/man/seqnamesTabix.Rd
Rsamtools/man/testPairedEndBam.Rd
Rsamtools/man/zip.Rd
Rsamtools/src
Rsamtools/src/BamFileIterator.h
Rsamtools/src/BamIterator.h
Rsamtools/src/BamRangeIterator.h
Rsamtools/src/Biostrings_stubs.c
Rsamtools/src/GenomicPosition.h
Rsamtools/src/IRanges_stubs.c
Rsamtools/src/Makevars
Rsamtools/src/Makevars.common
Rsamtools/src/Makevars.win
Rsamtools/src/PileupBuffer.cpp
Rsamtools/src/PileupBuffer.h
Rsamtools/src/PileupBufferShim.h
Rsamtools/src/PosCache.h
Rsamtools/src/PosCacheColl.cpp
Rsamtools/src/PosCacheColl.h
Rsamtools/src/R_init_Rsamtools.c
Rsamtools/src/ResultManager.cpp
Rsamtools/src/ResultManager.h
Rsamtools/src/S4Vectors_stubs.c
Rsamtools/src/Template.h
Rsamtools/src/XVector_stubs.c
Rsamtools/src/as_bam.c
Rsamtools/src/as_bam.h
Rsamtools/src/bam_data.c
Rsamtools/src/bam_data.h
Rsamtools/src/bam_mate_iter.cpp
Rsamtools/src/bam_mate_iter.h
Rsamtools/src/bambuffer.c
Rsamtools/src/bambuffer.h
Rsamtools/src/bamfile.c
Rsamtools/src/bamfile.h
Rsamtools/src/bcffile.c
Rsamtools/src/bcffile.h
Rsamtools/src/encode.c
Rsamtools/src/encode.h
Rsamtools/src/fafile.c
Rsamtools/src/fafile.h
Rsamtools/src/idxstats.c
Rsamtools/src/idxstats.h
Rsamtools/src/io_sam.c
Rsamtools/src/io_sam.h
Rsamtools/src/pbuffer_wrapper.cpp
Rsamtools/src/pbuffer_wrapper.h
Rsamtools/src/pileup.cpp
Rsamtools/src/pileup.h
Rsamtools/src/pileupbam.c
Rsamtools/src/pileupbam.h
Rsamtools/src/samtools
Rsamtools/src/samtools/bam.c
Rsamtools/src/samtools/bam.h
Rsamtools/src/samtools/bam_aux.c
Rsamtools/src/samtools/bam_endian.h
Rsamtools/src/samtools/bam_import.c
Rsamtools/src/samtools/bam_index.c
Rsamtools/src/samtools/bam_lpileup.c
Rsamtools/src/samtools/bam_md.c
Rsamtools/src/samtools/bam_pileup.c
Rsamtools/src/samtools/bam_reheader.c
Rsamtools/src/samtools/bam_sort.c
Rsamtools/src/samtools/bcftools
Rsamtools/src/samtools/bcftools/bcf.c
Rsamtools/src/samtools/bcftools/bcf.h
Rsamtools/src/samtools/bcftools/bcf2qcall.c
Rsamtools/src/samtools/bcftools/bcfutils.c
Rsamtools/src/samtools/bcftools/fet.c
Rsamtools/src/samtools/bcftools/index.c
Rsamtools/src/samtools/bcftools/prob1.c
Rsamtools/src/samtools/bcftools/prob1.h
Rsamtools/src/samtools/bcftools/vcf.c
Rsamtools/src/samtools/bgzf.c
Rsamtools/src/samtools/bgzf.h
Rsamtools/src/samtools/faidx.c
Rsamtools/src/samtools/faidx.h
Rsamtools/src/samtools/kaln.h
Rsamtools/src/samtools/khash.h
Rsamtools/src/samtools/knetfile.c
Rsamtools/src/samtools/knetfile.h
Rsamtools/src/samtools/kprobaln.c
Rsamtools/src/samtools/kprobaln.h
Rsamtools/src/samtools/kseq.h
Rsamtools/src/samtools/ksort.h
Rsamtools/src/samtools/kstring.c
Rsamtools/src/samtools/kstring.h
Rsamtools/src/samtools/razf.c
Rsamtools/src/samtools/razf.h
Rsamtools/src/samtools/sam.c
Rsamtools/src/samtools/sam.h
Rsamtools/src/samtools/sam_header.c
Rsamtools/src/samtools/sam_header.h
Rsamtools/src/samtools_patch.c
Rsamtools/src/samtools_patch.h
Rsamtools/src/scan_bam_data.c
Rsamtools/src/scan_bam_data.h
Rsamtools/src/tabix
Rsamtools/src/tabix/bedidx.c
Rsamtools/src/tabix/index.c
Rsamtools/src/tabix/tabix.h
Rsamtools/src/tabixfile.c
Rsamtools/src/tabixfile.h
Rsamtools/src/tagfilter.c
Rsamtools/src/tagfilter.h
Rsamtools/src/utilities.c
Rsamtools/src/utilities.h
Rsamtools/src/zip_compression.c
Rsamtools/src/zip_compression.h
Rsamtools/tests
Rsamtools/tests/Rsamtools_unit_tests.R
Rsamtools/vignettes
Rsamtools/vignettes/Rsamtools-Overview.Rnw
Rsamtools/vignettes/Rsamtools-UsingCLibraries.Rnw