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KISSNP2(1) User Commands KISSNP2(1)


kissnp2 - detects SNPs and indels from read sets


[Kissnp2 options]

(0 arg) : keep truncated bubbles, that have no successors on the 2 paths at the same position
(1 arg) : maximal number of polymorphism per bubble [default '1']
(1 arg) : maximal size of a predicted indel [default '0']
Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants
(1 arg) : input file (likely a hdf5 file)
(1 arg) : File (.h5) generated by kissnp2, containing the coverage threshold per read set [default '_removemeplease']
(1 arg) : output name
(0 arg) : extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with -t
(0 arg) : extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with -T
In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit [default '-1']
(1 arg) : branching mode
0: forbid SNPs for which any of the two paths is branching (high precision, low recall) 1: forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value) 2: No limitation on branching (low precision, high recall) [default '1']
(1 arg) : Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output [default '20']
(0 arg) : conserve low complexity SNPs
(1 arg) : number of cores [default '0']
(1 arg) : verbosity level [default '1']
(0 arg) : version
(0 arg) : help
(1 arg) : maximum depth for BFS [default '200']
(1 arg) : maximum breadth for BFS [default '20']


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

January 2019 kissnp2 2.3.0