{"repo":"PGScatalog/pgsc_calc","free":true,"listed":false,"github":"https://github.com/PGScatalog/pgsc_calc","clone":"git clone https://github.com/PGScatalog/pgsc_calc.git","description":"The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation","language":"Nextflow","stars":174,"topics":["polygenic-scores","polygenic-risk-scores","genetic-risk-score","pgs-catalog","nextflow","workflow","pgs","prs","polygenic-risk-score","polygenic-score"],"license":"Apache-2.0","category":"workflow-automation","readme_excerpt":"The Polygenic Score Catalog Calculator ( pgsc calc ) Introduction pgsc calc is a bioinformatics best-practice analysis pipeline for calculating polygenic [risk] scores on samples with imputed genotypes using existing scoring files from the Polygenic Score (PGS) Catalog and/or user-defined PGS/PRS. [!TIP] Working with large cloud-based environments like UK Biobank RAP or All of Us? Try our new pre-release with improved cloud compatibility for BGEN / VCF files Pipeline summary [!IMPORTANT] Whole genome sequencing (WGS) data are not currently supported by the calculator It’s possible to create compatible gVCFs from WGS data. We plan to improve support for WGS data in the near future. The workflow performs the following steps: Downloading scoring files using the PGS Catalog API in a specified genome build (GRCh37 and GRCh38). Reading custom scoring files (and performing a liftover if genotyping data is in a different build). Automatically combines and creates scoring files for efficient parallel computation of multiple PGS - Matching variants in the scoring files against variants in the target dataset (in plink bfile/pfile or VCF format) Calculates PGS for all samples (linear sum of weights and dosages) Creates a summary report to visualize score distributions and pipeline metadata (variant matching QC) And optionally: - Genetic Ancestry: calculate similarity of target samples to populations in a reference dataset (1000 Genomes (1000G)), using principal components analysis (PCA) ","default_branch":null,"files":null,"tree":[],"storefront":"/r/PGScatalog","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/PGScatalog/pgsc_calc/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}