removeDup(1) a component of subread suite


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.