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

6       samtools rmdup - removes duplicate reads (obsolete)
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SYNOPSIS

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

13       This command is obsolete. Use markdup instead.
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15       Remove  potential PCR duplicates: if multiple read pairs have identical
16       external coordinates, only retain the pair with highest  mapping  qual‐
17       ity.   In the paired-end mode, this command ONLY works with FR orienta‐
18       tion and requires ISIZE is correctly set. It does not work for unpaired
19       reads (e.g. two ends mapped to different chromosomes or orphan reads).
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OPTIONS

23       -s      Remove duplicates for single-end reads. By default, the command
24               works for paired-end reads only.
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26       -S      Treat paired-end reads and single-end reads.
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LIMITATIONS

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

37       Written by Heng Li from the Sanger Institute.
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SEE ALSO

41       samtools(1)
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43       Samtools website: <http://www.htslib.org/>
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47samtools-1.13                     7 July 2021                samtools-rmdup(1)