Meta-analysis software:


METAL: https://genome.sph.umich.edu/wiki/METAL_Documentation


PLINK: https://zzz.bwh.harvard.edu/plink/metaanal.shtml


Metasoft: http://genetics.cs.ucla.edu/meta/


GWAMA / MR_MEGA: https://genomics.ut.ee/en/tools


META: https://mathgen.stats.ox.ac.uk/genetics_software/meta/meta.html


Meta-analysis methods:


GWAS meta-analysis methods overview from 2008
https://pmc.ncbi.nlm.nih.gov/articles/PMC2782358/


GWAMA manuscript
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-288


MR-MEGA manuscript
https://academic.oup.com/hmg/article/26/18/3639/3976569#115627882


MetaSoft modified random effects and binary effects
https://www.cell.com/ajhg/fulltext/S0002-9297(11)00155-8
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002555


SmetABF
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009948


MANTRA
https://onlinelibrary.wiley.com/doi/10.1002/gepi.20630


MTAG
https://pubmed.ncbi.nlm.nih.gov/29292387/


MAMA
https://www.biorxiv.org/content/10.1101/2021.04.23.441003v1.full


Summary statistics alignment


GWAS summary stats formatting: https://github.com/MRCIEU/gwas-vcf-specification


MungeSumstats: https://www.bioconductor.org/packages/release/bioc/html/MungeSumstats.html
 
BCFtools score github repository: https://github.com/freeseek/score
GWAS_VCF sumstat format, reference alignment, meta-analysis, and PRS


2024 BCFtools/Liftover paper: https://academic.oup.com/bioinformatics/article/40/2/btae038/7585532


EASY QC R package: https://www.uni-regensburg.de/medizin/epidemiologie-praeventivmedizin/genetische-epidemiologie/software/







Referenced meta-analyses 

GBMI website: https://www.globalbiobankmeta.org/
Flagship paper - https://www.medrxiv.org/content/10.1101/2021.11.19.21266436v1.full.pdf
Github repository: https://github.com/globalbiobankmeta/META_ANALYSIS

GWAS catalog: https://www.ebi.ac.uk/gwas/
GWAS count figure: https://academic.oup.com/nar/article/53/D1/D998/7893318