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**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
**transition has 2/3 probability
**Uniform prior for transition to transversion ratio (1:1)
**each transversion has 1/6 probability
*'''New implementation''': Alternative mutation model with uniform (uninformative) prior for transition to transversion ratio
**updated by Yancy Lo, 9/24/2012
**each mutation has a 1/3 probability
**add --uniformTsTv in command line to enable this alternative mutation model
**download glfSingle with this new implementation here: [[File:Generic-glfSingle-2013-09-25.tar.gz]]
== Download ==
== Download ==
