delta-filter − read a delta alignment file from either nucmer or promer and filters the alignments
delta−filter [options]<deltafile>
−1 |
1−to−1 alignment allowing for rearrangements (intersection of −r and −q alignments) |
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−g |
1−to−1 global alignment not allowing rearrangements |
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−h |
Display help information |
−i float
Set the minimum alignment identity [0, 100], default 0
−l int |
Set the minimum alignment length, default 0 |
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−m |
Many−to−many alignment allowing for rearrangements (union of −r and −q alignments) |
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−q |
Maps each position of each query to its best hit in the reference, allowing for reference overlaps |
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−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 |
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−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
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