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Abecasis Group Wiki

Welcome!

Welcome to our brand new 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. Quality control using FastQValidator, VerifyBamID, and BamValidator
6. C++ APIs for sequence analsysis using C++ Library: libStatGen
7. Meta-analyze single variants or genes: including tools for generating summary statistics rvtests, rare-metal-worker, annotating summary statistics TabAnno, and performing meta-analysis command line tool raremetal and R package RareMETALS.

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

SardiNIA - The SardiNIA longitudinal study of aging.

1000 Genomes Project Pilot 1 SNP Calling

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

Abecasis Group Meeting

3:00-4:30 p.m. on Mondays, room 2610, SPH I.