Genome Analysis Wiki wiki_db http://genome.sph.umich.edu/wiki/Main_Page MediaWiki 1.43.1 first-letter Media Special Talk User User talk Genome Analysis Wiki Genome Analysis Wiki talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 1 16408 16407 2023-03-23T20:06:05Z Administrator 164 Reverted edits by [[Special:Contributions/LaneBurgoyne120|LaneBurgoyne120]] ([[User talk:LaneBurgoyne120|talk]]) to last revision by [[User:Administrator|Administrator]] 16390 wikitext text/x-wiki <div id="mf-mainpage"> <!-- BANNER ACROSS TOP OF PAGE --> {| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" |- | 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> |} [[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]] <!-- 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]]--> == 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> rsqs9o1kwcg2z982bqtq4qk50ss1b2m