Abecasis Group Wiki
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Sequence Analysis Tools
We are developing several tools for the analysis of next generation sequence data.
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
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
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
Faculty in the group teach in a variety of formal and informal settings. Class notes and relevant discussion are archived here.