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Correction mode:
One of the options -aggressive, -moderate, -conservative or -expert
must be selected.
The -aggressive, -moderate and -conservative modes are presets of
the criteria by which it is decided if an observed discrepancy in
homopolymer length between reference and a read shall be corrected
or not. A description of the single criteria is provided by using
the -help+ option. The presets are equivalent to the following settings:
-aggressive -moderate -conservative
-hmin 3 3 3
-read-hmin 1 1 2
-altmax 1.00 0.99 0.80
-refmin 0.00 0.00 0.10
-mapqmin 0 10 21
-covmin 1 1 1
-clenmax unlimited unlimited unlimited
-allow-multiple yes yes no
The aggressive mode tries to maximize the sensitivity, the conservative
mode to minimize the false positives. An even more conservative set
of corrections can be achieved using the -ann option (see -help+).
The -expert mode allows to manually set each parameter; the default
values are the same as in the -conservative mode.
(Finally, for evaluation purposes only, the -state-of-truth mode can be used:
this mode assumes that the target sequence of the sequencing has been specified
as reference sequence and outputs an ideal list of corrections.)]])
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