pgs-calc-nf
Nextflow pipeline to calculate polygenic scores using pgs-calc
Requirements
- Nextflow:
curl -s https://get.nextflow.io | bash
- Docker
Installation
Build docker image before run the pipeline:
docker build -t lukfor/pgs-calc-nf . # don't ingore the dot here
Test the pipeline and the created docker image with test-data:
nextflow run main.nf \
--project test-project \
--genotypes_imputed "tests/data/*.vcf.gz" \
--genotypes_imputed_format "vcf" \
--genotypes_imputed_have_index false \
--genotypes_build "hg19" \
--scores "tests/data/*.csv"
--output output
Normalized score files from PGSCatalog can be downloaded from here.
Contact
Lukas Forer (@lukfor), Institute of Genetic Epidemiology, Medical University of Innsbruck
License
pgs-calc-nf is MIT Licensed.