Samcat

This tool reads a set of input files in SAM or BAM format and outputs the concatenation of them. If the output file name is omitted the result is written to stdout.

(c) Copyright in 2014 by David Weese.

Web Documentation for Samcat

Options

version-check
Turn this option off to disable version update notifications of the application.
bam
Use BAM format for standard output. Default: SAM.
verbose
Print some stats.

Input Ports

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Input SAM or BAM file (or - for stdin). [bam,sam,sam.bgzf,sam.gz]

Output Ports

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Output file name. [bam,sam,sam.bgzf,sam.gz]

Views

Samcat Std Output
The text sent to standard out during the execution of Samcat.
Samcat Error Output
The text sent to standard error during the execution of Samcat. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

Further Links

Developers

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