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.

**P(non-reference heterozygote) = 0.01 * 2/3

**P(non-reference heterozygote) = 0.01 * 2/3

**P(non-reference homozygote) = 0.01 * 1/3

**P(non-reference homozygote) = 0.01 * 1/3

*Two options of mutation model:

*Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants

**Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants

**transition has 2/3 probability

**Uniform prior for transition to transversion ratio (1:1)

 

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

**each mutation has a 1/3 probability

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

== Download ==

== Download ==