I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation? I'm trying to use the GCTA64, but I couldn't get it working. The documentation doesn't help much. At the end of the day, I want: 1 - Simulate Case/Control and/or quantitative phenotype 2 - Link it with a real SNP dataset (eg: 1000 Genomes) 3 - Conduct GWAS analysis using Plink and/or Hail.

Looking Hail's and Plink's tutorials for GWAS, I realised both use simulated phenotypes from real SNP data sources (1000 Genomes and HapMap, respectively), but how they created the datasets are beyond of the scope of the tutorials, thus not reported.

As mentioned before, I've tried gcta64, but no success. Here's what I've tried:

1 - Downloaded 1000 Genome sample from Plink page: Entire dataset as a single .tar.gz (1.12 GB) (A2 allele major, not ref, on chr3 before 15 Oct 2017)

2 - Tried to generate the simulate data by:

./gcta64  --bfile 1kGenomesP1/1kg_phase1_all/1kg_phase1_all --simu-qt  --simu-causal-loci causal.snplist  --simu-hsq 0.5 --simu-rep 3  --keep test
.indi.list --out 1kg_phase1_all

Error: Error: --keep test.indi.list not found.

Question: What should be the files:causal.snplist and test.indi.list? I know the propety name suggests what should be, but there's no example of file structure nowhere...

Btw - I apologise in advance if this is a too trivial question. I'm quite new at it. Appreciate your patience and help :)


These inputs are at least partially described in the GCTA documentation here.

An example of the causal.snplist is given as a 2-column file with causal SNPs and effect sizes.

No description of the test.indi.list is given but it is described elsewhere as merely a list of individual IDs to use in the analysis.

If you continue experiencing difficulties you might email the author as described here.

Of course, you should also keep in mind that there are potentially some drawbacks to the approach in terms of properly handling population stratification / cryptic population structure (for a helpful technical discussion with more references, see here).

  • $\begingroup$ Hi @maximilian-press, thanks for the answer. Unfortunatelly those links you shared don't help (excpt the last one, the links are the the documentation of the application, which I've already mentioned in the question as unhealpful). Do you have an pratical example to share? Perhaps a tutorial, or so? I strougled on it. Like: What should be the test in the command line? is it a VCF? Is it a bed, bim, fam? I'm afraid I will have to email the authour... I wish everything were in a github repository. Woould be easier to track previous issues/doubts... Thanks again for your help! $\endgroup$ – Bruno Ambrozio Nov 7 '19 at 10:15
  • $\begingroup$ @BrunoAmbrozio see @mgkrebbs comment above for --keep file format. it is again just a 2-column file. $\endgroup$ – Maximilian Press Nov 8 '19 at 4:56

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