GWAS code

This webpage contains documentation and advice on how to perform Quality control on SNP data from Genomwide Association Studies (GWAS), or more generally on any whole-genome genotyping data.  I will provide solutions based on publically-available open source software. I will use the PLINK program (http://pngu.mgh.harvard.edu/~purcell/plink) for GWAS analysis, I will use Unix/Linux text manipulation commands (e.g. awk, grep, head, tail, sort, join) for preparing text files for further analysis, and the R statistical package (http://www.r-project.org)  for additional analysis and graphics. These are not the only options available for performing these tasks, but they are commonly used.
 
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