HaplotypeCaller should be wrapped with stdwrap.sh
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
Most of the log information that is produced by HaplotypeCaller is written to
stderr. It also write some information to
stdout but it is not any interesting stuff. This means that the log is lost in case the program i successful (which is is most of the time). If we want to keep everything we should use the
stdwrap.sh script as a wrapper (as we already do for some other programs).