How long does it take to carry out the GWAS workflow?

Question

[s2060266]

Including these steps:

1. raw data format transformation for five companies
2. update positions for all SNPs to hg37 version
3. Quality control within companies
4. Pre-phasing (SHAPEIT2) and imputation (IMPUTE2) for all SNPs of each company
5. Perform GWAS using two logistic models for 27 phenotypes
6. Statistic and downstream bioinformatic analysis.
7. Estimation of genetic parameters (rg and hg).
8. 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?

[4galaxy77]

It will be quicker if you use up to date software - imput2 and shapeit2 are old and slow. Use the Michigan/Sanger imputatin server instead.

[cpad0112]

hg37 version  

typo ??

Answer 1

[zx8754]

Too many factors to give a good estimate, anything between a week and six months.

1000 samples GWAS is pretty small, below is my guesstimates:

1. using R/python/bash 1-5 days
2. liftover 1 day
3. QC 2-3 days
4. I'd use online services like Michigan Imputation Service, 1-3 days
5. R/SNPTEST 1-4 days
6. 1-30 days, this is too broad, hard to guess
7. no idea
8. 1-5 days

Most of the time will not be spent on coding/running the analysis, but for interpreting and finding the correct way of doing it. So each step might have many iterations.