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samtools-rmdup(1)	     Bioinformatics tools	     samtools-rmdup(1)

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       This command is obsolete.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	 qual-
       ity.   In the paired-end	mode, this command ONLY	works with FR orienta-
       tion 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.  or-
	 phan  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/>

samtools-1.10			6 December 2019		     samtools-rmdup(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | LIMITATIONS | AUTHOR | SEE ALSO

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