---
name: "kissnp2"
section: "1"
platform: "linux"
package: "discosnp"
version: "1:2.6.2-4+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kissnp2"
---

# kissnp2(1)

detects SNPs and indels from read sets

## 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.