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+j2s: Deriving stratified effects from joint models investigating Gene-Environment Interactions
+======
+
+The python3 script **j2s.py** allows for the estimation of genetic effect sizes in unexposed and exposed individuals separately from joint models investigating Gene-Environment interactions when the exposure is binary. A pre-print of the publication is available [here](https://www.biorxiv.org/content/10.1101/693218v1).
+
+Prerequisite
+------------
+
+To execute the script, python3 must be installed as weel as the following Python packages:
+  + pandas (version 0.22.0)
+  + numpy (version 1.13.3)
+  + scipy (version 0.19.1)
+
+Execution
+------------
+
+To use the script, type the following command:
+
+``` bash
+python3 INFILE N N_EXPOSED OUTFILE
+```
+
+with:
+  * INFILE is the path to the input file describing the summary statitics in the joint model,
+  * N is the total sample size,
+  * N_EXPO is the number of exposed (E = 1) individuals,
+  * OUTFILE is the path to the outputfile.
+
+Description of the input files
+------------
+
+The input file has 7 mandatory columns:
+  * the identifier of the variant (e.g rs number) labelled 'MarkerName'
+  * the main genetic effect size labelled 'Effect'
+  * the standard error of the main genetic effect size labelled 'StdErr'
+  * the interaction effect size labelled 'IntEffect'
+  * the standard error of the interaction effect size labelled 'IntStdErr'
+  * the covariance between the main genetic effect size and the interaction effect size labelled 'IntCov'
+  * the sample size of the variant labelled 'N'
+
+| MarkerName   | Effect   |StdErr       |IntEffect    |IntStdErr     |IntCov        |N       |
+| ------------ | -------- | ----------- | ----------- | ------------ | -------------| ------ |
+| rs1          | 0.06464  | 0.09853     | 0.03685     |  0.1539      | -0.009603    | 302478 |
+| rs2          | 0.1482   | 0.0439      | 0.1071      |  0.05265     | -0.001922    | 551772 |
+| rs3          | 0.2428   | 0.06389     | 0.1027      |  0.07648     | -0.004073    | 537523 |
+| rs4          | -0.1821  | 0.05173     | -0.06716    |  0.06105     | -0.002671    | 540537 |
+| rs4          | -0.1665  | 0.04127     | -0.05506    |  0.0498      | -0.001692    | 527550 |
+
+This format corresponds to the output of the METAL software performing the joint test ([Manning et al, 2011](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312394/))
+
+Short tutorial
+--------------
+
+
+Bug report / Help
+-----------------
+
+Please open an issue if you find a bug.
+
+Code of conduct
+---------------
+
+Please note that this project is released with a [Contributor Code of Conduct](https://gitlab.pasteur.fr/statistical-genetics/j2s/blob/master/code-of-conduct.md). By participating in this project you agree to abide by its terms.
+
+License
+-------
+
+This project is licensed under the MIT License - see the [LICENSE.md](https://gitlab.pasteur.fr/statistical-genetics/j2s/blob/master/LICENSE) file for details

code-of-conduct.md

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