NAME

       bamreset - reset BAM file to unaligned state

SYNOPSIS

       bamreset [options]

DESCRIPTION

       bamreset  reads  a  BAM  file  from  standard  input, transforms it to a pre aligned state and writes the
       resulting data to standard output as a BAM file.

       Resetting the file involves the following actions:

              Remove all SQ lines from the header.

              Set the sorting order to unknown

              Drop all non primary alignments

              Remove all auxiliary fields

              Mark all reads as unmapped and erase the mapping coordinates and template length fields

              Move all reads to the forward direction by applying reverse complements  as  necessary  such  that
              afterwards no reverse complement flags are set.

       The following key=value pairs can be given:

       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

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

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

       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 md5filename is 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 indexfilename is unset, then no BAM index will be computed.

       indexfilename file name for BAM index if index=1.

       resetheadertext  file  name  for  replacement SAM header. By default the header of the input SAM/BAM/CRAM
       file is filtered.

       exclude=<SECONDARY,SUPPLEMENTARY>: Do not include reads in the output that have any of  the  given  flags
       set. The flags are given separated by commas. Valid flags are:

       PAIRED:
              read was paired in sequencing

       PROPER_PAIR:
              read has been mapped as part of a proper pair

       UNMAP: read was not mapped

       MUNMAP:
              mate of read was not mapped

       REVERSE:
              read was mapped to the reverse strand

       MREVERSE:
              mate of read was mapped to the reverse strand

       READ1: read was first read of a pair during sequencing

       READ2: read was second read of a pair during sequencing

       SECONDARY:
              alignment is secondary, i.e. an alternative mapping to the primary alignment in the same file

       QCFAIL:
              read as marked as having failed quality control

       DUP:   read is marked as a duplicate of another read in the same file (see bammarkduplicates)

       SUPPLEMENTARY:
              read is marked as supplementary alignment

       resetaux=<0|1>: auxiliary fields (default).

       resetsortorder=<0|1>:  set  sort order to unknown if resetsortorder=1 (default) and leave as it is in the
       input if resetsortorder=0.

       auxfilter=<>: comma separated list of aux tags to be kept if resetaux=0. If  the  key  is  not  set  when
       resetaux=0, then all tags are kept.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.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.

BIOBAMBAM                                           July 2013                                        BAMRESET(1)