Contributed Software

This section contains examples of projects contributed by users. TheSNPPit does support direct interaction with the underlying database. This gives users the possibility to write their own software that uses the infrastructure provided by TheSNPPit.

 

Parentage Testing

An example of user contributed software that uses TheSNPPit is the package Parentage Testing written by Hermann Schwarzenbacher (schwarzenbacher<at>zuchtdata.at).

The package Parentage Testing can be downloaded as a gzipped tar-archive from here. The archive contains a README file explaining the content of the package. The following list gives a brief overview of the content

 

  1. A short description is contained in the file readme.txt
  2. A bash script parentage.shand two R-scripts parentage.r and functions_verify.r which are called from the bash script.
  3. An example dataset consisting of
    • anims.ped: pedigree
    • candidates.txt: candidates for the pedigree check
    • data.map: mapping file
    • data.ped: genotype file
    • isag_disc.txt: ISAG markers for parentage discovery
    • isag_veri.txt: ISAG markers for parentage verification

 Performance

Parentage verification on a pedigree with 95.538 animals can be done in 4 seconds. Parentage discovery on the same pedigree takes about 38 minutes and requires about 1 GB of RAM.