Man page - removedup(1)

Packages contains this manual

Package:  subread
apt-get install subread

Manuals in package:
• sublong(1)
• subread-buildindex(1)
• repair(1)
• subread-fullscan(1)
• subindel(1)
• propmapped(1)
• subjunc(1)
• subread-align(1)
Documentations in package:
• subread

Manual

REMOVEDUP

NAME
DESCRIPTION
Usage:
AUTHOR

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NAME

removeDup - toolkit for processing next-gen sequencing data

DESCRIPTION

removeDup Version 2.0.4

Remove duplicated reads.

Usage:

./removeDup [options] -i <input_file> -o <output_file>

Required arguments:

	-i <string> Name of input file in SAM/BAM format.
	-o <string> Name of output SAM file including filtered reads. The format is

BAM unless ’-S’ is specified.

Optional arguments:

	-S
			Generate the SAM format output.

-r <int>

Specify the duplication cutoff. All the reads mapped to a location are removed from the output if the number of reads mapped to this location is equal or higher than the cutoff. 10 by default.

-t <string> A directory storing temporary files generated by the program.

AUTHOR

This manpage was written by Alexandre Mestiashvili for the Debian distribution and
can be used for any other usage of the program.

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