covid19hg/saige repository overview

COVID-19 Host Genetics Initiative SAIGE

This image contains the preferred SAIGE software to run GWAS for COVID-19 HGI. See https://github.com/weizhouUMICH/SAIGE⁠ for the repository.

Commands can be called: step1_fitNULLGLMM.R --help step2_SPAtests.R --help createSparseGRM.R --help

This image also contains a tool for QQ and Manhattan plotting:

qqplot.R --file SUMSTAT_FILE --chrcol CHR --bp_col POS --pval_col p.value

where --file is a summary stat text file and --chrcol, --bp_col and --pval_col chromosome, position and p-value column names in the file The output is png files for plots: QQ, Manhattan and Manhattan where p-values < 1e-10 are plotted on a log-log scale