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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 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:
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.