Provided by: discosnp_2.4.3-1_amd64
kissnp2 - detects SNPs and indels from read sets
[Kissnp2 options] -x (0 arg) : keep truncated bubbles, that have no successors on the 2 paths at the same position -P (1 arg) : maximal number of polymorphism per bubble [default '1'] -D (1 arg) : maximal size of a predicted indel [default '0'] -dont_output_first_coverage (0 arg) : Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants -in (1 arg) : input file (likely a hdf5 file) -coverage_file (1 arg) : File (.h5) generated by kissnp2, containing the coverage threshold per read set [default '_removemeplease'] -out (1 arg) : output name -T (0 arg) : extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with -t -t (0 arg) : extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with -T -max_symmetrical_crossroads (1 arg) : In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit [default '-1'] -b (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'] -max_ambigous_indel (1 arg) : Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output [default '20'] -l (0 arg) : conserve low complexity SNPs -nb-cores (1 arg) : number of cores [default '0'] -verbose (1 arg) : verbosity level [default '1'] -version (0 arg) : version -help (0 arg) : help -bfs-max-depth (1 arg) : maximum depth for BFS [default '200'] -bfs-max-breadth (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.