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Rsamtools

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

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Functions (27)

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.

FaFile-class

Manipulate indexed fasta files.

PileupFiles-class

Represent BAM files for pileup summaries.

Rsamtools-package

'samtools' aligned sequence utilities interface

RsamtoolsFile-class

A base class for managing file references in Rsamtools

RsamtoolsFileList-class

A base class for managing lists of Rsamtools file references

ScanBamParam-class

Parameters for scanning BAM files

ScanBcfParam-class

Parameters for scanning BCF files

TabixFile-class

Manipulate tabix indexed tab-delimited files.

applyPileups

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

defunct

Rsamtools Deprecated and Defunct

deprecated

Deprecated functions

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 statistics for a BAM file.

quickBamFlagSummary

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

readPileup

Import samtools 'pileup' files.

scanBam

Import, count, index, filter, sort, and merge ‘BAM’ (binary alignment) files.

scanBcf

Operations on ‘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.

testPairedEndBam

Quickly test if a BAM file has paired end reads

zip

File compression for tabix (bgzip) and fasta (razip) files. IMPORTANT NOTE: Starting with Rsamtools 1.99.0 (Bioconductor 3.9), razip() is defunct. Please use bgzip() instead.

Rsamtools

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

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release

Rsamtools

Functions (27)

Rsamtools

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