skyclub3 / burchardlab_tutorials

Burchardlab Tutorials

Pagé Goddard

I have set up this repository as a catch-all for the notes I make as I learn new programs and design pipelines. My Tutorials will focus on the codes I have used successfully with notes about what needed troubleshooting. I have attempted to make these walkthorughs clear and accurate with helpful details not included in the available vignettes.

• ADMIXTURE - used to estimate global genetic ancestry; walkthrough of a supervised admixed run on African Americans
• BASH Commands - navigating the server; basic bash commands for navigation, finding and viewing data; also detaching screens for backgrounf processes
• GENESES_PCRelate - used to estimate relatedness measurements in sample; genetic relatedness matrix generation
• GRM Methods Comparison - evaluates Pro's and Con's of 3 common GRM computation programs (GENESIS, REAP, GCTA) and conlcudes that GENESIS is the most robust for admixed populations
• Markdown - quick summary of markdown syntax used to create the following files
• PLINK_QC - intro to running quality control for genotype array data in PLINK to prepare for GWAS; example shown is the process used for the telomere project
• Useful_databases - a dynamic and curated list for different bioinfomatic databases by data type / research question

forthcoming:

• PLINK_GWAS
• PARIS_pathway_analysis