EvoGen_course

Evolutionary Genomics course - Data Analysis module

13th-17th April 2015

Material

To download all the material in this web page use git:

git clone https://github.com/mfumagalli/EvoGen_course

Enter the folder and create a subfolder "Work" where you will be running the exercises:

cd EvoGen_course
mkdir Work
cd Work
mkdir Results # you results will be saved here

Instructions to download remaining input files and to obatin necessary programs for the practical sessions are given here.

Feel free to contact me (mfumagalli82@gmail.com) if you have problems.

Agenda

Day 1

• Lecture: From raw NGS data to genotypes (slides)

• Paper discussion: (slides) and (paper)

• Practical session:

  • data filtering

  •   [genotype calling](https://github.com/mfumagalli/EvoGen_course/tree/master/Files/genocall.md)
    

• Additional material:

  •   genotype calling using:
    

    • SAMtools
    • BEAGLE

Day 2

• Lecture: SNP calling and advanced methods for evolutionary inferences from NGS data (slides)

• Paper discussion: (slides) and (papers)

• Practical session:

  •   [SNP calling](https://github.com/mfumagalli/EvoGen_course/tree/master/Files/snpcall.md)
    

  • advanced methods to estimate SFS

• Additional material:

  •   SNP calling using [SAMtools](https://github.com/mfumagalli/EvoGen_course/tree/master/Files/snpcall_samtools.md)
    

  • estimation of inbreeding coefficients
  • advanced methods to calculate summary statistics using:
    • ANGSD
    • ngsTools
    • ngsTools/ngsDist

Day 3

• Lecture: Population structure and demographic inferences (slides)

• Paper discussion: (slides) and (paper)

• Practical exercises:

  • estimating demographic parameters through simulations (R script)
  • inference of population splits and mixture events using TreeMix (bash script)

Day 4

• Lecture: Detecting natural selection (slides)

• Paper discussion: slides (pdf) and (paper)

• Practical exercises:

  • selection scan in the human genome and assessment of significance (R script)
  • summary statistics using ngsTools/ngsDist

Day 5

Evaluation.

Credits

Some materials have been borrowed (and then adapted) from Thorfinn Korneliussen, Anders Albrechtsen, Tyler Linderoth, Filipe G. Vieira. Sequencing data on butterfiles has been kindly provided by Zach Gompert. ANGSD has been developed by Thorfinn Korneliussen and Anders Albrechtsen. Filipe G. Vieira implemented the inbreeding estimation. Tyler Linderoth wrote most of data filtering scripts together with Sonal Singhai, Ke Bi, and Filipe G. Vieira.