NAME

       bammarkduplicates2 - mark duplicate reads/alignments in BAM files

SYNOPSIS

       bammarkduplicates2 [options]

DESCRIPTION

       bammarkduplicates2 reads a coordinate sorted BAM file containing alignments computed by an
       aligner, marks duplicate reads/alignments using the  coordinates  of  the  alignments  and
       writes  the  marked  alignments  to a BAM file. By default input is via standard input and
       output via standard output. Duplication metrics are provided on the standard error channel
       by  default.  bammarkduplicates2  scans the input BAM file twice, it is thus of benefit to
       set the I key (described below) to give the name of an input file. If the input  BAM  file
       is  given  via standard input, then a copy of the input will be stored in a temporary file
       during the first run for processing in a second run. bammarkduplicates2 assumes that  each
       read end of a pair occurs in exactly one entry in the file.

       The following key=value pairs can be given:

       I=<stdin>: name of the input file (input is read from standard input if not set). This key
       can be given multiple times. If it is given multiple times, then all the input files  need
       to  be  in coordinate sorted order and will be merged for output such that the output will
       be coordinate sorted.

       O=<stdout>: name of the output file (output is written to standard output if not set)

       M=<stderr>: name of the metrics file (metrics are written to standard error if not set)

       tmpfile=<filename>: prefix for temporary files. By default the temporary files are created
       in the current directory

       level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are

       -1:    zlib/gzip default compression level

       0:     uncompressed

       1:     zlib/gzip level 1 (fast) compression

       9:     zlib/gzip level 9 (best) compression

       If  libmaus  has  been compiled with support for igzip (see https://software.intel.com/en-
       us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-
       data) then an additional valid value is

       11:    igzip compression

       markthreads=<1>: Number of threads used during marking duplicate alignments.

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       mod=<1048576>:  print progress after processing every mod'th input read/alignment (default
       is 1M)

       rewritebam=<0|1|2>: compression type of the temporary file stored if I key  is  not  given
       (input is via standard input). Valid values are

       0:     temporary    data    is    compressed    using    snappy    (if    available,   see
              http://code.google.com/p/snappy/)

       1:     gzip/BAM, recompress input and store it as a BAM file

       2:     copy, produce a 1/1 copy of the input stream as a temporary file

       rewritebamlevel=<-1|0|1|9|11>: compression level of temporary BAM file if rewritebam is  1
       (see level key for possible values).

       colhashbits=<20>: base two logarithm of the size of the hash table used for collation (the
       default value is 18 and should work reasonably well for most input files.  Please see  the
       biobambam paper at arxiv.org/abs/1306.0836 for details).

       collistsize=<33554432>:  size  of  hash table overflow list in bytes (the default is 128MB
       and should work reasonably well for most input files. Please see the  biobambam  paper  at
       arxiv.org/abs/1306.0836 for details).

       fragbufsize=<50331648>:    size    of    each   fragment/pair   file   buffer   in   bytes
       (bammarkduplicates2 uses two such buffer for detecting duplicates)

       rmdup=<0|1>: sets how duplicates are handled

       0:     duplicates will be retained in the output file and have the duplication flag set

       1:     duplicates will be remove when writing the output file

       maxreadlength=<[500]>: maximum read length in input. This value can be set higher than the
       actual maximum in the file but not lower.

       md5=<0|1>: md5 checksum creation for output file. Valid values are

       0:     do not compute checksum. This is the default.

       1:     compute  checksum.  If  the md5filename key is set, then the checksum is written to
              the given file. If the md5filename key is not given  but  set  O  key  is  set  the
              checksum  will  be  written as output file name with .md5 appended.  If md5filename
              and O are unset, then no checksum will be computed.

       md5filename file name for md5 checksum if md5=1.

       index=<0|1>: compute BAM index for output file. Valid values are

       0:     do not compute BAM index. This is the default.

       1:     compute BAM index. If the indexfilename key is set, then the BAM index  is  written
              to  the  given file. If the indexfilename key is not given but set O key is set the
              checksum will be written as output file name with .bai appended.  If  indexfilename
              and O are unset, then no BAM index will be computed.

       indexfilename file name for BAM index if index=1.

       tag=<tag>  name  of auxiliary field storing tag information in string form. Read fragments
       or pairs with different tags will not be considered as  duplicates,  even  they  would  be
       according  to  their mapping coordinates. For pairs the tag field information of the first
       and second mate are concatenated to obtain the tag of the pair.

       nucltag=<tag> this option works like the tag option but  is  restricted  to  sequences  of
       nucleotides (A,C,G or T) as tags. The length of each tag sequence is not allowed to exceed
       15 bases. All tags are required to have the same length.  Each non  nucleotide  symbol  is
       mapped  to  A. In constrast to the tag option, nucltag uses less memory for processing and
       can be expected to be faster.

       D ouptut file name for removed duplicates if rmdup=1. By default the reads and read  pairs
       marked as duplicates are discarded when rmdup=1. If the D key is set, then the sequence of
       reads which is not written to the output file is written to a separate file. The  name  of
       this separate file is the value of the D key.

       dupmd5=<0|1>:  compute  md5  checksum of file given by D key if rmdup=1. By default no md5
       checksum is computed for this file.

       dupmd5filename: file name for storing the md5 checksum of the D file if rmdup=1, D is  set
       and dupmd5=1.

       dupindex=<0|1>:  compute BAM index for file given by D key if rmdup=1. By default no index
       is compute for this file.

       dupindexfilename: file name for storing the BAM index of the D file if rmdup=1, D  is  set
       and dupmd5=1.

       optminpixeldif=<100>:  distance  (x  and  y  inside  same  tile)  inside  which  reads are
       considered as optical duplicates

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <tischler@mpi-cbg.de>

COPYRIGHT

       Copyright © 2009-2013 German Tischler,  ©  2011-2013  Genome  Research  Limited.   License
       GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
       This  is free software: you are free to change and redistribute it.  There is NO WARRANTY,
       to the extent permitted by law.