In this repository one can find the code that was written for the genomic passport project carried out at the Fellay Lab at EPFL.
This notebook contains a walkthrough of the analysis pipeline that was implemented in the main.py files, to explain the steps that were taken to obtain the appropriate results.
This files contains the pharmacogenomic recommendation data that was used for the project.
- total_var_ann.csv contains drug recommendations over all variants, takent from the PharmGKB database.
- HLA_var_ann.csv contains drug recommendations from the same database but only for HLA alleles.
This files contains a list of all relevant SNP's that are in the drug recommendation database, as to be able to extract them using Plink software, and to speed up the subsequent analysis with Python.
These two files are necessary for the R script needed to perform the HIBAG method for HLA imputation. It relies on a classifier designed by a group at the University of Washington. The code also relies on a Bioconductor HIBAG library.
Automatized analysis pipeline. It was codod with Python 3.5.2
Input : patientName.vcf , 23&Me genotype data
How to run the program (From the Terminal)
python main.py -f patientName.vcf
Folder where the results of the pipeline are stored. One folder per day with one folder per patient.