bamtools
toolkit for manipulating BAM (genome alignment) files
Install
- All systems
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curl cmd.cat/bamtools.sh
- Debian
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apt-get install bamtools - Ubuntu
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apt-get install bamtools - Kali Linux
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apt-get install bamtools - Windows (WSL2)
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sudo apt-get updatesudo apt-get install bamtools - OS X
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brew install bamtools - Raspbian
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apt-get install bamtools - Dockerfile
- dockerfile.run/bamtools
bamtools
toolkit for manipulating BAM (genome alignment) files
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)