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


delta-filter [options]<deltafile>


-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

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