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Abecasis Group Wiki

Welcome!

Welcome to our brand new wiki!

If you would like to contribute, log-in or create 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 several tools for the analysis of next generation sequence data.

Read Mapping

Karma - Our fast short read aligner, which generates Mapping Quality Scores

Karma-ColorSpace - QUICKSTART on mapping color space reads

Examples - Sample command lines with discussion

Variant Calling

glfSingle - Variant calling for a single, deeply sequenced individual

glfTrio - Variant calling for a single, deeply sequenced nuclear family with two parents and one child

glfMultiples -- Variant calling for multiple, unrelated individuals

Variant Annotation

vcfCodingSnps -- Annotate coding variants in a VCF file.

Projects

SardiNIA - The SardiNIA longitudinal study of aging.

Learn Genetics

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

BIOSTAT 666: Statistical and Numerical Methods in Human Genetics

Gene mapping studies aim to study the relationship between genetic variation and susceptibility to human disease. These studies can be used to elucidate the biochemical basis of medically interesting traits leading to knowledge that will, ultimately, help us improve treatment and management of human disease.

Biostatistics 666 is a Masters level course that introduces many of the numerical methods and concepts useful for these types of study. Class Notes for this course posted in the wiki.