Changes

   --maxDepth      ''threshold''      Positions where the read depth exceeds this threshold will be excluded.

   --maxDepth      ''threshold''      Positions where the read depth exceeds this threshold will be excluded.

   --reference                    Positions called as homozygous reference will be included in the output.

   --reference                    Positions called as homozygous reference will be included in the output.

To learn about default values for these options, simply run the program with no arguments.

To learn about default values for these options, simply run the program with no arguments.

**each transversion has 1/6 probability

**each transversion has 1/6 probability

*New implementation: Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio

*'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio

**each mutation has a 1/3 probability

**each mutation has a 1/3 probability

**add --uniformTsTv in command line to enable this alternative mutation model

**add --uniformTsTv in command line to enable this alternative mutation model

**download here

**download glfSingle with this new implementation here: [[File:Generic-glfSingle-2013-09-25.tar.gz]]

== Download ==

== Download ==