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Sequence Analysis Tools
We are developing 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 FastQValidator, VerifyBamID, and BamValidator
- C++ APIs for sequence analsysis using C++ Library: libStatGen
- Meta-analysis of single variant or gene-level associations, including tools for generating summary statistics (Rvtests,RAREMETALWORKER), annotating summary statistics (TabAnno), and performing meta-analysis (command line tool RAREMETAL and R package RareMETALS).
- Sequencing study design helper Rarefy
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:
SardiNIA - The SardiNIA longitudinal study of aging.
Faculty in the group teach in a variety of formal and informal settings. Class notes and relevant discussion are archived here.