NAME

       samtools markdup - mark duplicate alignments in a coordinate sorted file

SYNOPSIS

       samtools  markdup  [-l  length]  [-r]  [-s]  [-T]  [-S]  [-f  file] [-d distance] [-c] [-t] [-m] [--mode]
       [--include-fails] [--no-PG] in.algsort.bam out.bam

DESCRIPTION

       Mark duplicate alignments from a coordinate sorted file that has been run through samtools  fixmate  with
       the -m option.  This program relies on the MC and ms tags that fixmate provides.

OPTIONS

       -l INT     Expected maximum read length of INT bases.  [300]

       -r         Remove duplicate reads.

       -s         Print some basic stats. See STATISTICS.

       -T PREFIX  Write temporary files to PREFIX.samtools.nnnn.mmmm.tmp

       -S         Mark supplementary reads of duplicates as duplicates.

       -f file    Write stats to named file.

       -d distance
                  The  optical duplicate distance.  Suggested settings of 100 for HiSeq style platforms or about
                  2500 for NovaSeq ones.  Default is 0 to not look for optical duplicates.  When set,  duplicate
                  reads  are  tagged  with dt:Z:SQ for optical duplicates and dt:Z:LB otherwise.  Calculation of
                  distance depends on coordinate data embedded in  the  read  names  produced  by  the  Illumina
                  sequencing machines.  Optical duplicate detection will not work on non standard names.

       -c         Clear previous duplicate settings and tags.

       -t         Mark duplicates with the name of the original in a do tag.

       -m, --mode TYPE
                  Duplicate  decision  method  for  paired reads.  Values are t or s.  Mode t measures positions
                  based on template start/end (default).  Mode s measures positions  based  on  sequence  start.
                  While  the  two  methods  identify mostly the same reads as duplicates, mode s tends to return
                  more results.  Unpaired reads are treated identically by both modes.

       --include-fails
                  Include quality checked failed reads.

       --no-PG    Do not add a PG line to the output file.

STATISTICS

       Entries are:
       COMMAND: the command line.
       READ: number of reads read in.
       WRITTEN: reads written out.
       EXCLUDED: reads ignored.  See below.
       EXAMINED: reads examined for duplication.
       PAIRED: reads that are part of a pair.
       SINGLE: reads that are not part of a pair.
       DUPLICATE PAIR: reads in a duplicate pair.
       DUPLICATE SINGLE: single read duplicates.
       DUPLICATE PAIR OPTICAL: optical duplicate paired reads.
       DUPLICATE SINGLE OPTICAL: optical duplicate single reads.
       DUPLICATE NON PRIMARY: supplementary/secondary duplicate reads.
       DUPLICATE NON PRIMARY OPTICAL: supplementary/secondary optical duplicate reads.
       DUPLICATE PRIMARY TOTAL: number of primary duplicate reads.
       DUPLICATE TOTAL: total number of duplicate reads.
       ESTIMATED LIBRARY SIZE: estimate of the number of unique fragments in the sequencing library.

       Estimated library size makes various assumptions e.g. the library consists of unique fragments  that  are
       randomly  selected  (with  replacement) with equal probability.  This is unlikely to be true in practice.
       However it can provide a useful guide into how many unique read pairs are likely  to  be  available.   In
       particular  it can be used to determine how much more data might be obtained by further sequencing of the
       library.

       Excluded reads are those marked as secondary, supplementary or unmapped.  By default QC failed reads  are
       also  excluded but can be included as an option.  Excluded reads are not used for calculating duplicates.
       They can optionally be marked as duplicates if they have a primary that is also a duplicate.

EXAMPLES

       This first command sort can be omitted if the file is already name ordered:

       samtools sort -n -o namesort.bam example.bam

       Add ms and MC tags for markdup to use later:

       samtools fixmate -m namesort.bam fixmate.bam

       Markdup needs position order:

       samtools sort -o positionsort.bam fixmate.bam

       Finally mark duplicates:

       samtools markdup positionsort.bam markdup.bam

AUTHOR

       Written by Andrew Whitwham from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-sort(1), samtools-fixmate(1)

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