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/>