Rsamtools v1.24.0

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

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.

Functions in Rsamtools

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