bamtools

toolkit for manipulating BAM (genome alignment) files

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.

BamTools provides both a C++ API for BAM file support as well as a command-line toolkit.

This is the bamtools command-line toolkit.

Available bamtools commands:

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)

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Homepage

https://github.com/pezmaster31/bamtools/wiki

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