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JasonTan-code authored Nov 15, 2023
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To perform linear regression on a (simulated) continuous phenotype in our admixed cohort, simply type the following command in your terminal:

```
python RunTractor.py --hapdose ADMIX_COHORT/ASW.phased --phe PHENO/Phe.txt --method linear --out SumStats.tsv
Rscript run_tractor.R --hapdose ADMIX_COHORT/ASW.phased --phe PHENO/Phe.txt --method linear --out SumStats.tsv
```

This generates our summary statistic output, which has the estimated ancestry-specific p value and effect sizes for each locus for each ancestry. More specifically, you shall see these columns in the summary statistics:
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