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
Rsamtools Deprecated and Defunct
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.
A base class for managing lists of Rsamtools file references
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
'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.
Parameters for scanning BCF files
Retrieve sequence names defined in a tabix file.
Manipulate tabix indexed tab-delimited files.