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       This command is obsolete.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/>