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Rsamtools (version 1.20.5)

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

Description

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.

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Version

Version

1.20.5

License

Artistic-2.0 | file LICENSE

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Rsamtools (1.20.5)

indexTabix

Compress and index tabix-compatible files.
applyPileups

Apply a user-provided function to calculate pile-up statistics across multiple BAM files.
BcfFile

Manipulate BCF files.
FaFile

Manipulate indexed fasta files.
deprecated

Deprecated functions
ApplyPileupsParam

Parameters for creating pileups from BAM files
headerTabix

Retrieve sequence names defined in a tabix file.
Deprecated and Defunct

Rsamtools Deprecated and Defunct
BamViews

Views into a set of BAM files
BamFile

Maintain and use BAM files
PileupFiles

Represent BAM files for pileup summaries.
RsamtoolsFile

A base class for managing file references in Rsamtools
RsamtoolsFileList

A base class for managing lists of Rsamtools file references
BcfInput

Operations on `BCF' files.
readPileup

Import samtools 'pileup' files.
Rsamtools-package

'samtools' aligned sequence utilities interface
pileup

Use filters and output formats to calculate pile-up statistics for a BAM file.
BamInput

Import, count, index, filter, sort, and merge `BAM' (binary alignment) files.
ScanBamParam

Parameters for scanning BAM files
quickBamFlagSummary

Group the records of a BAM file based on their flag bits and count the number of records in each group
Compression

File compression for tabix (bgzip) and fasta (razip) files.
TabixInput

Operations on `tabix' (indexed, tab-delimited) files.
seqnamesTabix

Retrieve sequence names defined in a tabix file.
FaInput

Operations on indexed 'fasta' files.
ScanBcfParam-class

Parameters for scanning BCF files
TabixFile

Manipulate tabix indexed tab-delimited files.
testPairedEndBam

Quickly test if a BAM file has paired end reads