NAME

removeDup - Remove duplicated reads

USAGE

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

Required arguments:

-i <string> Name of input file in SAM format.

-o <string> Name of output SAM file including filtered reads.

Aptional arguments:

-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.

-c <int>

The maximum number of reads the input file can have. 40 million by default.