Table 1.
Summary of available family-based analyses in ONETOOL
| Main | Sub-category | Detail |
|---|---|---|
| InfoQC analysis | Variant information | FST, Ts/Tv ratio, MAF, HWE, PCA |
| Sample information | Het, Het/Hom | |
| Pedigree information | Description and summary, plot, relative pairs | |
| Error detection | Mendelian error | |
| Relatedness matrix | Kinship, IBS, GRM | |
| Trait analysis | Familial aggregation | Correlation |
| Heritability | Based on Kinship, IBS, GRM | |
| Segregation analysis | Mode of inheritance | |
| Linkage analysis | Model-based | Two-point, utilizing segregation analysis |
| Model-free | Multipoint, modeling LD | |
| Association analysis | Single variant | Score test, TDT/SDT, MQLS, FQLS, EQLS, GEMMA |
| Gene-based | Collapsing, PEDCMC, FAMVT, FARVAT, FBSKAT, PEDGENE, RVTDT | |
| Genotype probability & dosage data | Scoretest, EQLS, GEMMA, CMC, PEDCMC, FAMVT, FARVAT, PEDGENE |