Main Page

Abecasis Group Wiki

Welcome!

Welcome to our wiki!

If you would like to contribute, log-in or request an account. We recommend using your e-mail address or Michigan uniqname as your user id.

For basic instructions, see the Wikipedia Tutorial.

Sequence Analysis Tools

We are developing software tools for the analysis of next generation sequence data.

These tools include:

1. Variant Calling with GlfSingle and GlfMultiples
2. Variant Calling and De Novo Mutation Detection in Families with Polymutt
3. Variant Annotations using VcfCodingSnps
4. Rare Variant Analysis using RvTests
5. Rare Variant Association Analysis in family samples FamRvTest
6. Quality control using FastQValidator, VerifyBamID, and BamValidator
7. C++ APIs for sequence analsysis using C++ Library: libStatGen
8. Meta-analysis of single variant or gene-level associations RAREMETAL-SOFTWARE
9. Sequencing study design helper Rarefy
10. Local ancestry inference (ancestry painting) using off-targeted sequence data SEQMIX
11. Association Container Toolbox EPACTS
12. 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:

1. Evaluating a Read Mapper on Simulated Data
2. SNP Call Set Properties
3. Generic Exome Analysis Plan

Projects

NHLBI Genome Sequencing Project

SardiNIA - The SardiNIA longitudinal study of aging.

Exome Meta-analysis of Drinking and Smoking (EMADS)

The 1000 Genomes Project

Learn Genetics

Faculty in the group teach in a variety of formal and informal settings. Class notes and relevant discussion are archived here.

General Resources

• Computer How-Tos