Rare variant tests

From Genome Analysis Wiki
Revision as of 21:05, 4 February 2011 by Cristen (talk | contribs) (Created page with '=== 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 ? i…')
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

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