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.

kissnp2 2.3.0                                     January 2019                                        KISSNP2(1)