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Conda enviroment:

VCftools, Bcftools, Plink, Eagle=v.. Python >3.5 pip libraries: pandas, Numpy, Scipy openssl=v1.0.2

merge.py -

Phasing and imputing the subject vcf file from 23andMe, Ancestry, or FTDNA

imputation_pipeline.py -

Using 1000 Genomes Reference DNA and input subject vcf file to create a PCA for determining user ancestry

PCA.sh - KNN.py -

Chicken pox, Shingles, Cold sores, Mononucleosis, Mumps, Hepatitis B, HIV, TB, Strep throat, Yeast Infections, Childhood ear infections

Extracting SNPs from the imputed subject vcf file pertaining to the Infections we are interested in merge.py -

Generating PRS Score has follwoing two steps:

1. Getting Valid SNPs for every Infection by Clumping and Threshold using Plink
2. Getting PRS score for every Infection using the above Valid SNPs

PRS.py -

percentile.py -