Ubuntu Manpage: removeDup – Remove duplicated reads

Provided by: subread_2.0.0+dfsg-1_amd64 bug


NAME

       removeDup - 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.

       ERROR: The input file is neither a BAM file nor a SAM file.

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