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=== 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'''
{| width="75%" cellspacing="0" cellpadding="5" border="1"
|-
! scope="col" align="left" | Test Name
! scope="col" align="left" | Reference
! scope="col" align="left" | Software
! scope="col" align="left" | 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 ||
|-
|}
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'''
{| width="75%" cellspacing="0" cellpadding="5" border="1"
|-
! scope="col" align="left" | Test Name
! scope="col" align="left" | Reference
! scope="col" align="left" | Software
! scope="col" align="left" | 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 ||
|-
|}
