H3AGWAS: a portable workflow for genome wide association studies

BMC Bioinformatics

Table 4 Non-exhaustive list of workflows that perform QC, association testing and/or post-association analysis of GWAS

Software	Analysis	Link
GWASTools (Bioconductor)	QC	https://www.bioconductor.org/packages/release/bioc/html/GWASTools.html, [45]
BigGWAS	QC, Association testing	https://github.com/ikmb/gwas-assoc, [44]
plinkQC	QC	https://meyer-lab-cshl.github.io/plinkQC/articles/plinkQC.html, [46]
GWAS-ellingson	QC	https://github.com/sallyrose0425/GWAS, [47]
TASSEL	Association testing with general linear model and mixed linear model approaches, some post analysis analysis	https://avikarn.com/2019-07-22-GWAS/, [48]
CAUSALdb-finemapping	Fine-mapping using different software	https://github.com/mulinlab/CAUSALdb-finemapping-pip, [49, 50]
FINNGEN	Fine-mapping	https://github.com/FINNGEN/finemapping-pipeline
FUMA	Post-association analysis using web interface	https://fuma.ctglab.nl/, [51, 52]
postgap	Post-association analysis with annotation through cis-regulatory data sets using python	https://github.com/Ensembl/postgap, [53]
nf-gwas-pipeline	QC, Association testing integrating R packages SNPRelate/GENESIS/GMMAT and ANNOVAR using Nextflow	https://github.com/montilab/nf-gwas-pipeline [54]
gwasglue	Post-association analysis with colocalisation, fine-mapping Mendelian randomisation using R	https://mrcieu.github.io/gwasglue

ISSN: 1471-2105