xenial (1) delta-filter.1.gz

Provided by: mummer_3.23~dfsg-3_amd64 bug

NAME

       delta-filter - read a delta alignment file from either nucmer or promer and filters the alignments

SYNOPSIS

       delta-filter [options]<deltafile>

DESCRIPTION

       -1     1-to-1 alignment allowing for rearrangements (intersection of -r and -q alignments)

       -g     1-to-1 global alignment not allowing rearrangements

       -h     Display help information

       -i float
              Set the minimum alignment identity [0, 100], default 0

       -l int Set the minimum alignment length, default 0

       -m     Many-to-many alignment allowing for rearrangements (union of -r and -q alignments)

       -q     Maps each position of each query to its best hit in the reference, allowing for reference overlaps

       -r     Maps each position of each reference to its best hit in the query, allowing for query overlaps

       -u float      Set the minimum alignment uniqueness, i.e. percent of

              the alignment matching to unique reference AND query sequence [0, 100], default 0

       -o float
              Set  the  maximum alignment overlap for -r and -q options as a percent of the alignment length [0,
              100], default 100

       -v     Print the discarded alignments instead of those that pass filters

       -b     Maps duplications (XOR of -r and -q alignments, one or the other but not both)

       Reads a delta alignment file from either nucmer or  promer  and  filters  the  alignments  based  on  the
       command-line  switches,  leaving only the desired alignments which are output to stdout in the same delta
       format as the input. For multiple switches, order of operations is as follows: -i -l -u -q -r  -g  -m  -1
       -b.  If  an  alignment  is  excluded  by  a  preceding  operation,  it  will be ignored by the succeeding
       operations.

       An important distinction between the -g option and the  -1  and  -m  options  is  that  -g  requires  the
       alignments  to  be mutually consistent in their order, while the -1 and -m options are not required to be
       mutually consistent and therefore tolerate translocations, inversions, etc.  In  general  cases,  the  -m
       option  is  the best choice, however -1 can be handy for applications such as SNP finding which require a
       1-to-1 mapping. Finally, for mapping query contigs, or sequencing reads, to a reference genome,  use  -q.
       The  duplications  printed with the -b option are -r and -q alignments that are not present in the 1-to-1
       alignment. These alignments are also the difference between the -1 and -m alignments

SEE ALSO

       The -b option originates from mugsy that provides a code copy of mummer  with  additional  patches.   The
       source can be found in SVN svn://svn.code.sf.net/p/mugsy/code/trunk