NAME

       samtools-rmdup - removes duplicate reads (obsolete)

SYNOPSIS

       samtools rmdup [-sS] input.srt.bam out.bam

DESCRIPTION

       This command is obsolete. Use markdup instead.

       Remove   potential  PCR  duplicates:  if  multiple  read  pairs  have  identical  external
       coordinates, only retain the pair with highest mapping quality.  In the  paired-end  mode,
       this  command  ONLY works with FR orientation and requires ISIZE is correctly set. It does
       not work for unpaired reads (e.g. two ends  mapped  to  different  chromosomes  or  orphan
       reads).

OPTIONS

       -s      Remove  duplicates for single-end reads. By default, the command works for paired-
               end reads only.

       -S      Treat paired-end reads and single-end reads.

LIMITATIONS

       o Samtools paired-end rmdup does not work for unpaired reads (e.g. orphan  reads  or  ends
         mapped   to   different  chromosomes).  If  this  is  a  concern,  please  use  Picard's
         MarkDuplicates which correctly handles these cases, although a little slower.

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1)

       Samtools website: <http://www.htslib.org/>