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.