Setp 2: Generate Plink bfiles (.bim, .bam, .fam)

After filtering SNPs in GWAS summary statistics data. Users have to generate plink files for generate PRS model.

Function: `gprs generate-plink-bfiles`

This option encodes plink1.9 make-bed function

plink --vcf [ref] --extract [snplists after qc] --make-bed --out [bfile folder/output_name]

How to use it?

Shell:

$ gprs generate-plink-bfiles --ref [str] --snplist_name [str] --symbol [str] --output_name [str]

Python:

from gprs.gene_atlas_model import GeneAtlasModel

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

    geneatlas.generate_plink_bfiles(snplist_name='2014height_MEC', output_name='2014height_hg38',extra_commands="--vcf-half-call r" ,symbol='_GRCh38.genotypes')

output files

*.bim
*.bed
*.fam