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

DELTA-FILTER(1) User Commands DELTA-FILTER(1)

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
April 2015 mummer 3.23