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| ! scope="col" align="left" | Notes | | ! scope="col" align="left" | Notes |
| |- | | |- |
− | | CMC/T1 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | CMC/T1 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] |
| + | | |
| + | | [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |- | | |- |
− | | KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] || |
| + | | [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |- | | |- |
− | | VT* || [http://www.ncbi.nlm.nih.gov/pubmed/20471002 Price et al., 2010] || http://genetics.bwh.harvard.edu/rare_variants/ || Incorporating functional weights but not VT, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | VT* || [http://www.ncbi.nlm.nih.gov/pubmed/20471002 Price et al., 2010] |
| + | | http://genetics.bwh.harvard.edu/rare_variants/ |
| + | | Incorporating functional weights but not VT, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | |
| |- | | |- |
− | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || |
| + | | with 1% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |- | | |- |
− | | CMAT || [http://www.ncbi.nlm.nih.gov/pubmed/21070896 Zawistowski et al. 2010] || || | | + | | CMAT || [http://www.ncbi.nlm.nih.gov/pubmed/21070896 Zawistowski et al. 2010] || || |
| |- | | |- |
− | | ANRV/GRANVIL* || [http://www.ncbi.nlm.nih.gov/pubmed/19810025 Morris & Zeggini] || || | | + | | ANRV/GRANVIL* || [http://www.ncbi.nlm.nih.gov/pubmed/19810025 Morris & Zeggini] || || |
| |- | | |- |
− | | RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || | | + | | RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || |
| |- | | |- |
− | | CCRaVAT and QuTie* || [http://www.ncbi.nlm.nih.gov/pubmed/20964851 Lawrence et al. 2010] || http://www.sanger.ac.uk/resources/software/rarevariant/ || | | + | | CCRaVAT and QuTie* || [http://www.ncbi.nlm.nih.gov/pubmed/20964851 Lawrence et al. 2010] |
| + | | http://www.sanger.ac.uk/resources/software/rarevariant/ || |
| |- | | |- |
− | | RVE (rare variant exclusive) || Cohen & Hobb || || underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | RVE (rare variant exclusive) || Cohen & Hobbs || |
| + | | underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |} | | |} |
| | | |
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| ! scope="col" align="left" | Notes | | ! scope="col" align="left" | Notes |
| |- | | |- |
− | | C-alpha || [Neale et al., submitted] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | C-alpha || [Neale et al., submitted] || |
| + | | [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |- | | |- |
− | | Ionita-Laza & Lange || [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001289 Ionita-Laza & Lange, 2011] || || | | + | | Ionita-Laza & Lange |
| + | | [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001289 Ionita-Laza & Lange, 2011] || || | |
| |- | | |- |
− | | DASH* || [http://www.ncbi.nlm.nih.gov/pubmed/20413981 Han & Pan] || || Computational burden | | + | | DASH* || [http://www.ncbi.nlm.nih.gov/pubmed/20413981 Han & Pan] || || Computational burden |
| |- | | |- |
− | | SKAT* || [http://www.ncbi.nlm.nih.gov/pubmed/20560208 Wu et al., 2010] || http://www.hsph.harvard.edu/~xlin/software.html || For some kernel choices, need to code 0=major homozygote, 1=het, 2-minor homozygote | | + | | SKAT* || [http://www.ncbi.nlm.nih.gov/pubmed/20560208 Wu et al., 2010] |
| + | | http://www.hsph.harvard.edu/~xlin/software.html |
| + | | For some kernel choices, need to code 0=major homozygote, 1=het, 2-minor homozygote |
| |- | | |- |
− | | WHaIT || [http://www.ncbi.nlm.nih.gov/pubmed/21055717 Li et al. 2010] || http://www.sph.umich.edu/csg/yli/whait/ || | | + | | WHaIT || [http://www.ncbi.nlm.nih.gov/pubmed/21055717 Li et al. 2010] |
| + | | http://www.sph.umich.edu/csg/yli/whait/ || |
| |- | | |- |
− | | EMMPAT* || [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978703/pdf/pgen.1001202.pdf King et al. 2010] || http://home.uchicago.edu/~crk8e/papersup.html || | | + | | EMMPAT* |
| + | | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978703/pdf/pgen.1001202.pdf King et al. 2010] |
| + | | http://home.uchicago.edu/~crk8e/papersup.html || |
| |} | | |} |
| | | |
Line 115: |
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| ! scope="col" align="left" | Notes | | ! scope="col" align="left" | Notes |
| |- | | |- |
− | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% or 5% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || |
| + | | with 1% or 5% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |- | | |- |
− | | RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || | | + | | RARECOVER |
| + | | [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || |
| |- | | |- |
− | | Step-Up Collapsing* || [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 Hoffman et al. 2010] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | Step-Up Collapsing* |
| + | | [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 Hoffman et al. 2010] || |
| + | | [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |- | | |- |
− | | CMC/T5 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | + | | CMC/T5 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] || |
| + | | [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| |- | | |- |
− | | MENDEL* || [http://www.ncbi.nlm.nih.gov/pubmed/21121038 Zhou et al. 2011] || http://www.genetics.ucla.edu/software/download?package=1 || | | + | | MENDEL* || [http://www.ncbi.nlm.nih.gov/pubmed/21121038 Zhou et al. 2011] |
| + | | http://www.genetics.ucla.edu/software/download?package=1 || |
| |} | | |} |
| | | |
Line 141: |
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| ! scope="col" align="left" | Notes | | ! scope="col" align="left" | Notes |
| |- | | |- |
− | | Logic regression* || [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] || || | | + | | Logic regression* || [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] || || |
| |- | | |- |
− | | Sequence diversity || Anderson et al. 2006 || || | | + | | Sequence diversity || Anderson et al. 2006 || || |
| |- | | |- |
− | | Sequence dissimilarity* || Schork et al. 2008, Wessel et al. 2006 || || | | + | | Sequence dissimilarity* || Schork et al. 2008, Wessel et al. 2006 || || |
| |- | | |- |
− | | Ridge regression * || Malo et al. 2008 || || | | + | | Ridge regression * || Malo et al. 2008 || || |
| |} | | |} |