.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH REMOVEDUP "1" "February 2020" "removeDup 2.0.0+dfsg-1~bpo10+1" "User Commands"
.SH NAME
removeDup \- Remove duplicated reads
.SH USAGE
.PP
removeDup [options] \fB\-i\fR <input_file> \fB\-o\fR <output_file>
.PP
Required arguments:
.HP
\fB\-i\fR <string> Name of input file in SAM/BAM format.
.HP
\fB\-o\fR <string> Name of output SAM file including filtered reads. The format is
.IP
BAM unless '\-S' is specified.
.PP
Optional arguments:
.TP
\fB\-S\fR
Generate the SAM format output.
.TP
\fB\-r\fR <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.
.HP
\fB\-t\fR <string> A directory storing temporary files generated by the program.
.PP
ERROR: The input file is neither a BAM file nor a SAM file.