Skip to main content

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