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DELTA-FILTER

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

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