Genome wide association studies (GWAS) are hypothesis-free methods for identifying associations between genetic regions and traits. GWAS analysis are usually used to identify genes involved in human disease.
By applying GWAS analysis to variant data we will be able to identify a given variant (or a set of variants) involved in a given phenotype or disorder.Based on a statistical test, GWAS analysis will provide a level of significance (or p-value) for each variant.
OpenCGA implements GWAS analysis where users can specify the statistical test: chi square and fisher.
In OpenCGA, a GWAS analysis returns a text file that consists of a header line (starting with #), and then one line per variant with the following 12-13 columns:
Start base-pair coordinate
End base-pair coordinate
List of consequence types
Allelic test chi-square statistic. Not present with 'fisher' test.