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Rsamtools (version 1.18.3)

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

1.18.3

License

Artistic-2.0 | file LICENSE

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Rsamtools (1.18.3)

Manipulate BCF files.

Manipulate indexed fasta files.

Deprecated functions

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

Sample from a BAM files

Deprecated and Defunct

Rsamtools Deprecated and Defunct

ApplyPileupsParam

Parameters for creating pileups from BAM files

Maintain and use BAM files

Retrieve sequence names defined in a tabix file.

Views into a set of BAM files

Represent BAM files for pileup summaries.

RsamtoolsFileList

A base class for managing lists of Rsamtools file references

quickBamFlagSummary

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

A base class for managing file references in Rsamtools

Import samtools 'pileup' files.

Compress and index tabix-compatible files.

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

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

Parameters for scanning BAM files

Rsamtools-package

'samtools' aligned sequence utilities interface

Operations on `BCF' files.

Operations on indexed 'fasta' files.

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

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

ScanBcfParam-class

Parameters for scanning BCF files

Retrieve sequence names defined in a tabix file.

Manipulate tabix indexed tab-delimited files.