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 |