BLUPF90

The course was held at UGA May 15 - June 1, 2012. Instructors were Ignacy Misztal, Shogo Tsuruta, Ignacio Aguilar, Zulma Vitezica & Andres Legarra.

1. Introduction to programming in Fortran 95/2003
2. Advance Programming in Fortran 95/2005
3. Computer algorithms useful in animal breeding
4. Efficient creation and solving of mixed model equations

Lectures by Ignacy Misztal. Labs by Shogo Tsuruta and Ignacio Aguilar

See class notes and the exercises

1. Introduction to BLUPF90 family of programs (Ignacy Misztal)
2. Properties of different algorithms for parameter estimation; EM and AI REML; simple and optimized Gibbs Samplers (Ignacy Misztal and Shogo Tsuruta)
3. Exercise: use of programs for data set with 1 -3 -7 traits. See last exercise in exercises above.

1. Introduction to genomic selection: LD, simple models (Andres Legarra)
2. Data simulation (including genomics) (Zulma Vitezica)
3. Methods based on SNP estimation (BLUP_SNP and BayesCPi etc.) (Andres Legarra)
4. Exercise: Data simulation and analysis using above models. Optional exercise.

1. Genomic relationship matrix (Andres Legarra)
2. Creation and handling of genomic relationship matrices with preGSf90 (Ignacio Aguilar)
3. GBLUP, GREML and GGIBBBS using blupf90 etc. This is included in the talks by Andres Legarra and Ignacio Aguilar.
4. Exercise: use of above programs with simulated and mice data

1. Theory of Single-step (Andres Legarra)
2. Single Step for populations under selection. Bias, inflation, accuracy (Zulma Vitezica)
3. Forming Single Step equations and quality control (Ignacio Aguilar)
4. Exercises: single step with simulated data set (Ignacio Aguilar & Daniela Lino) Files
5. Guest lecture: Issues related with genomic selection: the effect of selection, IBS matrices, and analysis of poultry data (Bill Muir)

1. Guest lecture: Practical results with Single Step (Selma Forni)
2. GWAS in Single Step (Huiyu Wang -Joy)
3. Experiences and future with ssGBLUP (Ignacy Misztal)
4. Exercises: GWAS exercises (Huiyu Wang & Ignacio Aguilar) Files

Zipped files can be found here:

1. ex_qmsim
2. mice_data_R
3. mice_cours
4. QMSim_UGA
5. Single-Step
6. ssGWAS