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Welcome to our brand new wiki!

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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.

Quality Control Utilities

FastQ Validator -- Check that a FASTQ file conforms to specification.

FastQFile -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read.

BamIdentityCheck -- Check that mapped reads are consistent with known genotypes for each individual.

Other Useful Links


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.