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,BAMPE,BEDPE}]
              [-g  GSIZE]  [-s  TSIZE]  [-p  PVALUE]  [--keep-dup  KEEPDUPLICATES]  [--buffer-size  BUFFER_SIZE]
              [--verbose VERBOSE] [--outdir OUTDIR] [-o OUTPUTFILE] [-d]

   options:
       -h, --help
              show this help message and exit

       -i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
              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,BAMPE,BEDPE}, --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}
              Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or
              "BOWTIE"  or  "BAMPE"  or "BEDPE". 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 or BAMPE/BEDPE. 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 reads as 'PCR/Optical duplicate' in bit 1024, MACS2 will still read them although  the  reads
              may be decided by MACS2 as duplicate later. Default: auto

       --buffer-size BUFFER_SIZE
              Buffer size for incrementally increasing internal array size to store reads alignment information.
              In  most  cases,  you  don't have to change this parameter.  However, if there are large number of
              chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size
              in order to decrease memory usage (but it will take longer time to read alignment files).  Minimum
              memory  requested  for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes.
              DEFAULT: 100000

       --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. Note, if the input format
              is BAMPE or BEDPE, the output will be in BEDPE format. 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

macs2 filterdup 2.2.7.1                            April 2022                                 MACS2_FILTERDUP(1)