Table 1:
Software packages for Biobank-Scale Association Analysis. We compared the features of several widely used software packages that can analyze biobank scale datasets for associations. We considered the input file format supported, the type of phenotypes (binary or quantitative) they can analyze, the gene-level tests they can perform, as well as whether they can handle samples with relatedness.
| Software for Biobank- Scale Data Analysis |
BGENIE | BOLT-LMM | PLINK2 | RVTESTS | SAIGE |
|---|---|---|---|---|---|
| Input File Format |
BGEN | BGEN/PLINK/dosage/VCF | BGEN/PLINK/dosage/VCF | BGEN/VCF/PLINK | BGEN/VCF/dosage |
| Single Variant Association Analysis | |||||
| Quantitative Trait | ✓ | ✓ | ✓ | ✓ | ✓ |
| Binary trait | ✓ | ✓ | X (only Wald test) | ✓ (include correction for unbalanced case/control samples) | ✓ (include correction for unbalanced case/control samples) |
| Gene-level Association Test | |||||
| Simple burden; SKAT and Variable Threshold Test | X | X | X | ✓ | X |
| Support for Related Individuals and Linear Mixed Model Analysis | X | ✓ | X | ✓ | ✓ |
| Generation of Summary Statistics | X | X | X | ✓ | X |