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.
- -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.