#AAAGs 2018 AAAGs Bioinformatics Workshop Repository
August 1-3, 2018
University of Buffalo

Session 1
Topics: Task Automation - Version Control with Git
Instructor: Dr. Joanna Malukiewicz (German Primate Center, Instituto Adolfo Lutz, Universidade Federal do Vale São Franciso)
Info: Introduction to command line, version control, and automation.

Session 2
Topics: The Basics of Read Mapping and Variant Calling
Instructor: Dr. Tim Webster (Arizona State University and University of Utah)
Info: Introduction to sequencing reads (fastq files), read mapping (SAM/BAM files), and variant calling (VCF files). Topics also include read trimming and quality control, duplicate removal, and BAM file analysis and exploration. Run alignment pipeline starting with a raw fastq file and producing a raw VCF file.

Session 3
Topics: The Basics of VCF files
Instructor: Dr. Maria Nieves-Colón (Arizona State University and LANGEBIO-CINVESTAV)
Info: VCF format and introduction to variant filtering. Output data details: Filtered VCF files, SNP density, Fst, Tajima's D.
Run variant filtering and analysis pipeline starting with a raw VCF file and producing population genetic metrics from a filtered VCF.

Session 4
Topics: Data Management in R Instructor: Dr. Ellen Quillen (Wake Forest University)
Info: Basics of manipulating data in Tidy R, Tidyverse, Bioconductor, etc.

Session 5
Topics: Multiple Testing Correction With Large Datasets
Instructor: Christopher Clukay (University of Florida)
Info: Basics of multiple testing correction methods and selection
Optimize computing time by taking advantage of multiple processors

Session 6
Topics: Molecular genetic and genomic analysis of gene variants
Instructor: Dr. Antonio Herrera (Stony Brook University)
Info: Identifying sources of variation and the role of mutation in the evolution of DNA sequence and gene function. Using python, we will explore aspects of molecular genetic and genomic function of identified variants and generate hypotheses about their effect on gene function.

Session 7
Topics: Structural Variants and Haplotype Interval Matching
Instructors: Dr. Omer Gokcumen and Yen-Lung Onta Lin (University of Buffalo)
Info: Investigate genomic outliers and associated haplotypes for their impact on gene expression function, loss of function variants, etc.

Session 8
Topics: Admixture and Genetic Introgression Analysis
Instructor: Dr. Krishna Veeramah (Stony Brook University)
Info: Applying f and D statistics using the ADMIXTOOLS package to infer population admixture

Session 9
Topics: Data Visualization in R
Instructor: Dr. Genevieve Housman (University of Chicago)
Info: Basics of Visualizing Data in R using ggplot2 and Gviz