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| + | <div id="mf-mainpage"> |
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| + | | style="width:100%; text-align:center; white-space:nowrap; color:#000;" | <div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div> |
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| + | [[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]] |
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| + | <!-- Below are old images from 2009 and 2014 Retreats --> |
| + | <!-- <br> [[Image:Abecasis2015Retreat.JPG|700px|center|Group Photo 2015]] --> |
| + | <!-- <br> [[Image:Abecasis2014Retreat.JPG|700px|center|Group Photo 2014]] --> |
| + | <!-- <br> [[Image:2009.08 Group Retreat Photo.jpg|center|400px|Group Photo]]--> |
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| + | |
| + | == Welcome! == |
| + | |
| + | Welcome to our wiki! |
| + | |
| + | If you would like to contribute, [[Special:UserLogin|log-in]] or [[Special:RequestAccount|request an account]]. We recommend using your e-mail address or Michigan uniqname as your user id. |
| + | |
| + | For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial]. |
| + | |
| + | == Sequence Analysis Tools == |
| + | |
| + | We are developing [[Software|software tools]] for the analysis of next generation sequence data. |
| + | |
| + | These tools include: |
| + | |
| + | #Variant Calling with [[GlfSingle]] and [[GlfMultiples]] |
| + | #Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]] |
| + | #Variant Annotations using [[VcfCodingSnps]] |
| + | #Rare Variant Analysis using [[RvTests]] |
| + | #Rare Variant Association Analysis in family samples [[FamRvTest]] |
| + | #Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]] |
| + | #C++ APIs for sequence analsysis using [[C++ Library: libStatGen]] |
| + | #Meta-analysis of single variant or gene-level associations [[RAREMETAL-SOFTWARE]] |
| + | #Sequencing study design helper [[Rarefy]] |
| + | #Local ancestry inference (ancestry painting) using off-targeted sequence data [[SEQMIX]] |
| + | #Association Container Toolbox [[EPACTS]] |
| + | #Fast Genotype Imputation Tool : [[Minimac3]] |
| + | |
| + | These tools and additional tools can be found on the [[Software]] page. |
| + | |
| + | We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]] |
| + | |
| + | == High Level Tutorials == |
| + | |
| + | Some high-level tutorials on the analysis of next generation sequence data: |
| + | |
| + | #[[Evaluating a Read Mapper on Simulated Data]] |
| + | #[[SNP Call Set Properties]] |
| + | #[[Generic Exome Analysis Plan]] |
| + | |
| + | == Projects == |
| + | |
| + | [[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]] |
| + | |
| + | [[SardiNIA]] - The SardiNIA longitudinal study of aging. |
| + | |
| + | [[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]] |
| + | |
| + | [http://www.1000genomes.org The 1000 Genomes Project] |
| + | |
| + | == Learn Genetics == |
| + | |
| + | Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here. |
| + | |
| + | == General Resources == |
| + | |
| + | *[[Computer How-Tos]] |
| + | </div> |