From: H3AGWAS: a portable workflow for genome wide association studies
Software | Analysis | Link |
---|---|---|
GWASTools (Bioconductor) | QC | https://www.bioconductor.org/packages/release/bioc/html/GWASTools.html, [45] |
BigGWAS | QC, Association testing | |
plinkQC | QC | https://meyer-lab-cshl.github.io/plinkQC/articles/plinkQC.html, [46] |
GWAS-ellingson | QC | |
TASSEL | Association testing with general linear model and mixed linear model approaches, some post analysis analysis | |
CAUSALdb-finemapping | Fine-mapping using different software | https://github.com/mulinlab/CAUSALdb-finemapping-pip, [49, 50] |
FINNGEN | Fine-mapping | |
FUMA | Post-association analysis using web interface | |
postgap | Post-association analysis with annotation through cis-regulatory data sets using python | |
nf-gwas-pipeline | QC, Association testing integrating R packages SNPRelate/GENESIS/GMMAT and ANNOVAR using Nextflow | |
gwasglue | Post-association analysis with colocalisation, fine-mapping Mendelian randomisation using R |