PGS Calculator

Applying polygenic scores (PGS) on imputed genotypes

Features

command line program (works on linux or MacOS)
supports vcf.gz files (imputed or genotyped)
supports different filters (e.g. r2 or variant list)
supports PGS Catalog format (https://www.pgscatalog.org, currently over 2,000 scores)
creates an interactive html report

Installation

Download pgs-calc-*.tar.gz from latest release
Extract the downloaded archive (e.g tar -xf bash installer.sh)
Validate installation with ./pgs-calc --version

Usage

Applying polygenic scores (PGS) on imputed genotypes

./pgs-calc apply --ref PGS000018 --out PGS000018.scores.txt chr*.dose.noID.vcf.gz  --report-html PGS000018.html

All scores are written to file PGS000018.scores.txt and an interactive report html report is created.

Optional parameters

--minR2 <value> - Use only variants with an imputation quality (R2) >= <value>:
--writeVariants <file> - Writes csv file with all variants used in calculation
--includeVariants <file> - Restrict calculation to use only variants from this csv file
--genotypes GT|DS - Use genotypes or dosage
--report-html <file> - Creates an interactive html report. The report includes summary statistics (like coverage) for each score and can be filtered by e.g. id or trait.

Input files

Genotypes

VCF file format (*.vcf and *.vcf.gz)
one VCF file per chromosome (e.g. output of Imputationserver)
works out of the box with imputed genotypes from Michigan Imputation Server

Scores

./pgs-calc supports PGSCatalog out of the box: open the website, find your score of interest and download the provided txt.gz files.

Examples

Single chromosome

Apply PGS to a single file (e.g. one chromosome):

./pgs-calc apply --ref PGS000018.txt.gz test.chr1.vcf.gz --out scores.txt

All scores are written to file scores.txt

Multiple chromosomes

Apply PGS to multiple files (e.g. multiple chromosomes):

./pgs-calc apply --ref PGS000018.txt.gz test.chr1.vcf.gz test.chr2.vcf.gz test.chr3.vcf.gz test.chr4.vcf.gz --out scores.txt

Apply PGS to multiple files by using file patterns:

./pgs-calc apply --ref PGS000018.txt.gz test.chr*.vcf.gz --out scores.txt

Multiple scores

Apply multiple score files:

./pgs-calc apply --ref PGS000018.txt.gz,PGS000027.txt.gz test.chr*.vcf.gz --out scores.txt

Filter by Imputation Qualitity

Use only variants with an imputation quality (R2) >= 0.9:

./pgs-calc apply --ref PGS000018.txt.gz test.chr*.vcf.gz --minR2 0.9 --out scores.txt

PGSCatalog support

If a PGS id is provided, pgs-calc downloads the file from PGSCatalog automatically:

./pgs-calc apply --ref PGS000018 test.chr1.vcf.gz --out scores.txt