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/ | Incorporating functional weights but not VT | |
| WSS | Madsen & Browning, 2009 | with 1% cutoff | ||
| CMAT | Zawistowski et al. 2010 |
