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Line 1: − + − + − | style="width:100%; text-align:center; white-space:nowrap; color:#000;" | + − + + + + − + + + + + − + − + − + − + − + − + − === [[Read Mapping]] ===+ − + + + + + + + + + + + + − + − + − + − [[glfSingle]] - Variant calling for a single, deeply sequenced individual+ − + + + − [[glfMultiples]] -- Variant calling for multiple, unrelated individuals+ − === Variant Annotation ===+ − + − === Quality Control Utilities ===+ − + − [[FastQFile]] -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read. − [[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual. − − === [[Links to Sequence Analysis Tools|Other Useful Links]] === − − == Projects == − [[SardiNIA]] - The SardiNIA longitudinal study of aging.+ − + − + − Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.+ +
Reverted edits by LaneBurgoyne120 (talk) to last revision by Administrator
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<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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== Welcome! ==
== Welcome! ==
Welcome to our brand new wiki!
Welcome to our wiki!
If you would like to contribute, [[Special:UserLogin|log-in]] or [http://csgwiki.sph.umich.edu/index.php?title=Special:UserLogin&type=signup create 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.
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].
== Sequence Analysis Tools ==
== Sequence Analysis Tools ==
We are developing several tools for the analysis of next generation sequence data.
We are developing [[Software|software tools]] for the analysis of next generation sequence data.
These tools include:
[[Karma|Karma]] - Our fast short read aligner, which generates [[Mapping Quality Scores]]
#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]]
[[Karma-colorspace|Karma-ColorSpace]] - QUICKSTART on mapping color space reads
These tools and additional tools can be found on the [[Software]] page.
[[Examples|Examples]] - Sample command lines with discussion
We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]
=== Variant Calling ===
== High Level Tutorials ==
Some high-level tutorials on the analysis of next generation sequence data:
[[glfTrio]] - Variant calling for a single, deeply sequenced nuclear family with two parents and one child
#[[Evaluating a Read Mapper on Simulated Data]]
#[[SNP Call Set Properties]]
#[[Generic Exome Analysis Plan]]
== Projects ==
[[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]]
[[vcfCodingSnps]] -- Annotate coding variants in a VCF file.
[[SardiNIA]] - The SardiNIA longitudinal study of aging.
[[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]]
[[FastQ Validator]] -- Check that a FASTQ file conforms to specification.
[http://www.1000genomes.org The 1000 Genomes Project]
== Learn Genetics ==
[[1000 Genomes Project Pilot 1 SNP Calling]]
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 ==
== General Resources ==
*[[Computer How-Tos]]
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