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

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?

plink impute2 shapeit2 gwas gcta
• 2,633 views • link
updated by cpad0112 cpad0112 • written by s2060266 • s2060266

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.

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written by 4galaxy77 4galaxy77 
hg37 version

typo ??

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written by cpad0112 cpad0112

1 answer

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.

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written by zx8754 zx8754

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