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bamtools - Online in the Cloud

Run bamtools in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bamtools that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

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