Software
Downloadable Software/Scripts
Basic Tools: A list of basic perl scripts that are useful for manipulating sequence information in a more general fashion and creating a pipeline.
>These perl scripts are designed to be run from the Windows command-prompt (Vista/7) and have standard Unix/DOS-like options functunality (e.g. C:>script1.exe -i input.txt -o output.txt etc.).

>Both pre-packaged executables (exe) and code (pl) are available for most of the scripts. Executables are optimized for 64-bit Windows and may or may not function on 32-bit systems.

>All scripts include a help option (e.g. C:>script1.exe -h) for a general description of function followed by option list.

>Contact author for bugs, comments, or questions: jcv128@psu.edu
Notes:
Pipeline Scripts: A list of perl scripts that serve a primary and/or specific role in a sequence filtering and annotation pipeline.
PipeMeta Package: PipeMeta scripts.
Betas: Possibly useful but unfinished. Also home of SNPHunter, which is no longer really a beta.