NAME

       macs2_filterdup - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 filterdup [-h] -i IFILE [IFILE ...]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
              [-g  GSIZE]  [-s TSIZE] [-p PVALUE] [--keep-dup KEEPDUPLICATES] [--verbose VERBOSE]
              [--outdir OUTDIR] [-o OUTPUTFILE] [-d]

   optional arguments:
       -h, --help
              show this help message and exit

       -i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
              ChIP-seq alignment file. If multiple files are given as '-t A B C', then they  will
              all be read and combined. Note that pair-end data is not supposed to work with this
              command. REQUIRED.

       -f            {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE},             --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}
              Format  of  tag  file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or
              "SAM" or "BAM" or "BOWTIE". The default AUTO  option  will  let  'macs2  filterdup'
              decide  which format the file is. Please check the definition in README file if you
              choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: "AUTO"

       -g GSIZE, --gsize GSIZE
              Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for  human
              (2.7e9),  'mm'  for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly
              (1.2e8), DEFAULT:hs

       -s TSIZE, --tsize TSIZE
              Tag size. This will override the auto detected tag size. DEFAULT: Not set

       -p PVALUE, --pvalue PVALUE
              Pvalue cutoff for binomial distribution test.  DEFAULT:1e-5

       --keep-dup KEEPDUPLICATES
              It controls the 'macs2 filterdup' behavior  towards  duplicate  tags/pairs  at  the
              exact same location -- the same coordination and the same strand. The 'auto' option
              makes 'macs2 filterdup' calculate the maximum tags at the exact same location based
              on binomal distribution using given -p as pvalue cutoff; and the 'all' option keeps
              every tags (useful if you only want to convert formats). If an integer is given, at
              most  this  number of tags will be kept at the same location.  Note, MACS2 callpeak
              function uses KEEPDUPLICATES=1 as default. Note, if you've used samtools or  picard
              to  flag  duplicates  in  bit  1024,  MACS2 will discard them no matter how you set
              KEEPDUPLICATES. Default: auto

       --verbose VERBOSE
              Set verbose level. 0: only  show  critical  message,  1:  show  additional  warning
              message,  2:  show process information, 3: show debug messages. If you want to know
              where are the duplicate reads, use 3. DEFAULT:2

       --outdir OUTDIR
              If specified all output files will be  written  to  that  directory.  Default:  the
              current working directory

       -o OUTPUTFILE, --ofile OUTPUTFILE
              Output  BED  file  name.  If not specified, will write to standard output. DEFAULT:
              stdout

       -d, --dry-run
              When set, filterdup will only output  numbers  instead  of  writing  output  files,
              including  maximum  allowable  duplicates,  total number of reads before filtering,
              total number of reads after filtering, and redundant rate. Default: not set