H3AGWAS: a portable workflow for genome wide association studies

BMC Bioinformatics

Table 1 List of softwares and resources used in H3AGWAS workflow, softwares are classify by phase of GWAS and task

Phase	Software/resource	Workflow/task	References
All	PLINK (1.9)	All	[18]
	Python (3)	All	[9]
	R (3.6)	Plot and extraction data	[10]
Association testing	GEMMA (0.98.5)	Association testing/heritability/conditional analysis	[12]
	Fast-LMM (binary version)	Association testing	[11]
	BOLT-LMM	Association testing/heritability	[13]
	SAIGE 1.0	Association testing	[16]
	regenie 3.1.3	Association testing	[17]
	GCTA : fastGWA	Association testing	[14, 15]
Post-association analysis	GCTA: COJO-slct, simulation, GREML	Fine-mapping/heritability/simulation	[19]
	MetaSoft	Meta-analyses	[20]
	GWAMA	Meta-analyses	[21]
	METAL	Meta-analyses	[22]
	MTAG	Multi-trait association	[23]
	LDSC	Heritability	[24]
	PhenoSim	Simulation	[25]
	LocusZoom	Annotations	[26]
	Annovar	Annotations	[27]
Format data	BCFtools	Convert vcf	[28]
	QCTOOL (v2)	Convert vcf to bgen/bimbam/impute2	[29]
	CrossMap	Convert positions between genome builds	[30]

ISSN: 1471-2105