Including these steps:
- raw data format transformation for five companies
- update positions for all SNPs to hg37 version
- Quality control within companies
- Pre-phasing (SHAPEIT2) and imputation (IMPUTE2) for all SNPs of each company
- Perform GWAS using two logistic models for 27 phenotypes
- Statistic and downstream bioinformatic analysis.
- Estimation of genetic parameters (rg and hg).
- PRS analysis.
However. the size of my dataset only consist more than 1000 people. With no background knowledge, how long would this take as a bioinformatics master student?