Calculate polygenic risk score

1. Preprocessing data

1.1 Weights files

Check prs scoring files (for example, files from PGS Catalog) for errors:
script preprocess pgs/preprocess_prs_file.py,
see --help for help with arguments,
'PGS001833.txt' example in data/.

1.2 VCF files

Check your vcf file for SNPs IDs - rsIDs. To get more info to your vcf:

• VCF files can be annotated with oakvar
• VCF files can be annotated with bcftools, source of annotation can be selected from NCBI Human Variation Sets in VCF Format (ClinVar, dbSNP)
  See launch example in preprocess/annotate_vcf.sh

2. Calculate polygenic risk score

Check header of script calc_and_visualize/calc_prs.py: file paths to vcf and prs scoring file must be specified, to use the optional enable/disable some SNPs, the paths to these lists can be set.

3. Visualize

To draw bullet plot fill the data (custom_snp_number, overall_snp_number variables) in header calc_and_visualize/draw_bullet_plot.py and run.

3. Calculate PRS with plink

We can also perform additional check with plink.

3.1 Plink

• Get plink binary files by running the script preprocess/plink convert/get_plink_fileset_bin.sh.
  If get into troubles with getting binary fileset, some intermediate steps may help. See plink/get_plink_fileset_pgen.sh, plink/pgen_to_bed.sh, or just try to fix initial .vcf file.
  
• Run calc_and_visualize/run_plink_prs.sh

3.2 Plink2

• Get plink pfiles by running the script preprocess/plink convert/get_plink_fileset_pgen.sh.
• Run calc_and_visualize/run_plink2_prs.sh plink/run_plink_prs.sh