Rare variant tests
From Genome Analysis Wiki
Summary of rare variant tests for sequence data
Compiled by Cristen Willer and Suzanne Leal for the ESP Feb 1, 2011
* indicates applicability to quantitative data
? indicates possible applicability to quantitative data with adaptation Blue font indicates implementation in upcoming PLINKSeq release (http://atgu.mgh.harvard.edu/plinkseq/)
1) Aggregate tests using a cut off e.g. 1 % analyzing nonsynonymous variants to detect detrimental variants
| Test Name | Reference | Software | Notes | |
|---|---|---|---|
| CMC/T1 test* | Li & Leal, 2008 | ||
| KBAC | Liu & Leal, 2010 | ||
| VT* | Price et al., 2010 | http://genetics.bwh.harvard.edu/rare_variants/ | |
| WSS | Madsen & Browning, 2009 | ||
| CMAT | Zawistowski et al. 2010 | ||
| ANRV/GRANVIL* | Morris & Zeggini | ||
| RARECOVER | Bhati et al. 2010 | ||
| CCRaVAT and QuTie* | Lawrence et al. 2010 | http://www.sanger.ac.uk/resources/software/rarevariant/ | |
| RVE (rare variant exclusive) | Cohen & Hobb |
2) Aggregate tests for protective and detrimental variants (recommend 1% cutoff)
| Test Name | Reference | Software | Notes | |
|---|---|---|---|
| C-alpha | [Neale et al., submitted] | ||
| Ionita-Laza & Lange | Ionita-Laza & Lange, 2011 | ||
| DASH* | Han & Pan | ||
| SKAT* | Wu et al., 2010 | http://www.hsph.harvard.edu/~xlin/software.html | |
| WHaIT | Li et al. 2010 | http://www.sph.umich.edu/csg/yli/whait/ | |
| EMMPAT* | King et al. 2010 | http://home.uchicago.edu/~crk8e/papersup.html |
Analyzing common and rare variants together (could down-weight or threshold common variants)
| Test Name | Reference | Software | Notes | |
|---|---|---|---|
| WSS | Madsen & Browning, 2009 | ||
| RARECOVER | Bhati et al. 2010 | ||
| Step-Up Collapsing* | [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 |
