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− | <div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div> | + | {| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" |
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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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− | [[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]] | + | <!-- 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! == |
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− | Welcome to our brand new wiki! | + | Welcome to our wiki! |
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− | 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. | + | 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. |
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− | For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial]. | + | For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial]. |
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− | == Sequence Analysis Tools == | + | == Sequence Analysis Tools == |
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| We are developing [[Software|software tools]] for the analysis of next generation sequence data. | | We are developing [[Software|software tools]] for the analysis of next generation sequence data. |
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− | These tools include: | + | These tools include: |
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− | # Variant Calling with [[glfSingle]] and [[glfMultiples]] | + | #Variant Calling with [[GlfSingle]] and [[GlfMultiples]] |
− | # Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]] | + | #Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]] |
− | # Variant Annotations using [[vcfCodingSnps]] | + | #Variant Annotations using [[VcfCodingSnps]] |
− | # Rare Variant Analysis using [[rvTests]] | + | #Rare Variant Analysis using [[RvTests]] |
− | # Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]] | + | #Rare Variant Association Analysis in family samples [[FamRvTest]] |
− | # File Readers using [[LibStatGen: BAM]] and [[LibStatGen: FASTQ]] | + | #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]] |
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− | These tools and additional tools can be found on the [[Software]] page. | + | These tools and additional tools can be found on the [[Software]] page. |
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− | == High Level Tutorials ==
| + | We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]] |
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− | Some high-level tutorials on the analysis of next generation sequence data:
| + | == High Level Tutorials == |
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− | # [[Evaluating a Read Mapper on Simulated Data]] | + | Some high-level tutorials on the analysis of next generation sequence data: |
− | # [[SNP Call Set Properties]] | + | |
− | # [[Generic Exome Analysis Plan]] | + | #[[Evaluating a Read Mapper on Simulated Data]] |
| + | #[[SNP Call Set Properties]] |
| + | #[[Generic Exome Analysis Plan]] |
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| == Projects == | | == Projects == |
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− | [[SardiNIA]] - The SardiNIA longitudinal study of aging. | + | [[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]] |
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| + | [[SardiNIA]] - The SardiNIA longitudinal study of aging. |
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− | [[1000 Genomes Project Pilot 1 SNP Calling]] | + | [[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]] |
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− | == Learn Genetics ==
| + | [http://www.1000genomes.org The 1000 Genomes Project] |
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− | Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.
| + | == Learn Genetics == |
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− | == General Resources ==
| + | Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here. |
− | * [[Computer How-Tos]]
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− | ==Abecasis Group Meeting== | + | == General Resources == |
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− | 3:00-4:30 p.m. on Mondays, room 2610, SPH I.
| + | *[[Computer How-Tos]] |
| + | </div> |