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bamtools - toolkit for manipulating BAM (genome alignment) files

BAMTOOLS(1) User Commands BAMTOOLS(1)

NAME

bamtools - toolkit for manipulating BAM (genome alignment) files

SYNOPSIS

bamtools [--help] COMMAND [ARGS]

DESCRIPTION

BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

OPTIONS

convert
Converts between BAM and a number of other formats
count
Prints number of alignments in BAM file(s)
coverage
Prints coverage statistics from the input BAM file
filter
Filters BAM file(s) by user-specified criteria
header
Prints BAM header information
index
Generates index for BAM file
merge
Merge multiple BAM files into single file
random
Select random alignments from existing BAM file(s), intended more as a testing tool.
resolve
Resolves paired-end reads (marking the IsProperPair flag as needed)
revert
Removes duplicate marks and restores original base qualities
sort
Sorts the BAM file according to some criteria
split
Splits a BAM file on user-specified property, creating a new BAM output file for each value found
stats
Prints some basic statistics from input BAM file(s)
See 'bamtools help COMMAND' for more information on a specific command.
April 2014 bamtools 2.3.0+dfsg