NAME

       kissnp2 - detects SNPs and indels from read sets

DESCRIPTION

       [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']

AUTHOR

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