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Table 2 Comparison of available functions for existing toolsets

From: WISARD: workbench for integrated superfast association studies for related datasets

Category
 Functions
WISARD PLINK2 GCTA FREGAT Rvtests
Input format
 PED O O X X X
 Binary PED O O O O X
 VCF O O X O O
 Binary VCF O O X X X
 Dosage O O O X X
 Others O O X O X
 Random dataset O O X X X
Recode dataset
 PED O O X X X
 Binary PED O O O X X
 VCF O O X X X
 Binary VCF O O X X X
 Others O O O X X
Data manipulation
 # of variant filters 38 27 8 0 11
 # of gene filters 4 0 0 0 2
 # of subject filters 28 27 2 0 4
 Family-specific filters O X X X X
 VCF-specific filters O X X X O
 Data merge O O X X X
 Covariate filters O O X X X
 Data split O O X X X
Distance matrix
 # of input formats 4 1 1 0 1
 # of output formats 4 1 1 0 1
 # of producible distances 7 2 1 0 4
Data summary
 Variant summary O O X X X
 Gene summary functions O X X O X
Variant-level analysis of unrelated samples
 binary phenotypes O O O X O
 continuous phenotypes O O O X O
 multivariate phenotypes O O O X O
Gene-level analysis of unrelated samples
 binary phenotypes O O X O O
 continuous phenotypes O O X O O
 multivariate phenotypes O X X X O
 X-chromosome O X X X X
Variant-level analysis of related samples
 binary phenotypes O X O X O
 continuous phenotypes O X O X O
 multivariate phenotypes O X O X O
Gene-level analysis of related samples
 binary phenotypes O X X O O
 continuous phenotypes O X X O O
 multivariate phenotypes O X X X O
Others features
 Variant-level meta-analysis O O X X O
 Gene-level meta-analysis O X X X O
 R connectivity O O X O X
 Multi-thread analyses O O O O O
 Programming Language C/C++ C/C++ C/C++ R C/C++
 # of supported platforms 5 3 1 3 1