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delta-filter - Online in the Cloud

Run delta-filter in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command delta-filter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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