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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. File Readers using LibStatGen: BAM and LibStatGen: FASTQ
7. File Conversions using bam2FastQ

These tools and additional tools can be found on the Software page.

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.