Setp 4-1: Generate PRS model

Generate PRS model by using Dosage by plink2.0

Function: gprs build-prs

plink2 --vcf [vcf input] dosage=DS --score [snplists afte clumped and qc]  --out 

The clumped qc snpslists and prs_output_dir will automatically be filled in the script. Users have to indicate the options below.

How to use it?

Shell:

$ gprs build-prs --vcf_input [str] --qc_clump_snplist_foldername [str] --symbol [str/int] --columns [int] --plink_modifier [str] --memory [int] --clump_kb [int] --clump_p1 [float/scientific notation] --clump_r2 [float] --output_name [output name]

Python:

from gprs.gene_atlas_model import GeneAtlasModel

if __name__ == '__main__':
    geneatlas = GeneAtlasModel( ref='1000genomes/hg19',
                    data_dir='data/2014_GWAS_Height' )

    geneatlas.build_prs( vcf_input= '1000genomes/hg19',
                          output_name ='2014height', memory='1000',clump_kb='250',
                    clump_p1='0.02', clump_r2='0.02', qc_clump_snplist_foldername='2014height')

output files

• *.sscore

IID	ALLELE_CT	NAMED_ALLELE_DOSAGE_SUM
HG00096	130	116
HG00097	130	114
HG00099	130	119
HG00100	130	110

Setp 4-2: Combined PRS model

Combined PRS model (python script create by Soyoung Jeon; update by Ying-Chu Lo))

Function:gprs combine-prs

Combine-prs will combine all .sscore files as one .sscore file. And calculate score average and sum per individual.

How to use it?

Shell:

$ gprs combine-prs --ref [str] --result_dur [str] 

Python:

from gprs.gene_atlas_model import GeneAtlasModel

if __name__ == '__main__':
    geneatlas = GeneAtlasModel( ref='1000genomes/hg19',
                    data_dir='data/2014_GWAS_Height' )

    geneatlas.combine_prs(filename="2014height",clump_r2="0.5",clump_kb="250",clump_p1="0.02")

output files

• *.sscore

id	ALLELE_CT	SCORE_AVG	SCORE_SUM
HG03270	1872.0	-0.00109666512273	-2.2826939078
HG03271	1872.0	-0.00111419935	-2.2831272058
NA19670	1872.0	-0.00117191923182	-2.4014961794
HG03279	1872.0	-0.00115016386364	-2.3057819