Skip to main content
. 2022 Nov 19;23:498. doi: 10.1186/s12859-022-05034-w

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]