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Rsamtools (version 1.24.0)

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

1.24.0

License

Artistic-2.0 | file LICENSE

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Rsamtools (1.24.0)

Manipulate indexed fasta files.

Manipulate BCF files.

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

Parameters for scanning BAM files

ApplyPileupsParam

Parameters for creating pileups from BAM files

Views into a set of BAM files

Deprecated functions

RsamtoolsFileList

A base class for managing lists of Rsamtools file references

Retrieve sequence names defined in a tabix file.

Maintain and use BAM files

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

Operations on `BCF' files.

Represent BAM files for pileup summaries.

A base class for managing file references in Rsamtools

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

ScanBcfParam-class

Parameters for scanning BCF files

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

Retrieve sequence names defined in a tabix file.

Import samtools 'pileup' files.

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

Compress and index tabix-compatible files.

Manipulate tabix indexed tab-delimited files.

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