{"repo":"joonan-lab/cwas","free":true,"listed":false,"github":"https://github.com/joonan-lab/cwas","clone":"git clone https://github.com/joonan-lab/cwas.git","description":"Category-wide association study (CWAS) (Werling et al., 2018; An et al., 2018)","language":"Python","stars":11,"topics":["bioinformatics","data-pipeline","python"],"license":"MIT","category":"data-pipelines","readme_excerpt":"Category-wide association study (CWAS) CWAS (Category-Wide Association Study) is a data analytic tool to perform stringent association tests to find non-coding loci associated with autism spectrum disorder (ASD). CWAS runs category-based burden tests using de novo variants from whole genome sequencing data and diverse annotation data sets. CWAS was used in the following papers. - An analytical framework for whole genome sequence association studies and its implications for autism spectrum disorder (Werling et al. , 2018) - Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder (An et al. , 2018) - CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data (Kim et al. , 2024) Here is the original CWAS repository: sanderslab/cwas Quickstart Data requirements Users must prepare following data for CWAS because it is very essential but cannot be generated automatically. Here are details. 1. Input VCF data (De novo variant list) - The input VCF data must follow the specification of VCF. - The INFO field must contain a sample ID of each variant with this format SAMPLE={sample id} . 2. List of samples SAMPLE PHENOTYPE :------: :-------: 11000.p1 case 11000.s1 ctrl 11002.p1 case 11002.s1 ctrl - CWAS requires the file like above listing sample IDs with its family IDs and phenotypes (Case= case , Control= ctrl ). - Here are details of the required format. - Tab se","default_branch":null,"files":null,"tree":[],"storefront":"/r/joonan-lab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/joonan-lab/cwas/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."}