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Abecasis Group Wiki
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Welcome!
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
MapabilityScores - Definitions of various mappability scores adopted at UCSC genome browser.
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.
BamIdentityCheck -- Check that mapped reads are consistent with known genotypes for each individual.
File Readers
BamFile -- Reads a BAM/SAM file.
FastQFile -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
File Conversion
bam2FastQ -- Convert BAM files into FastQ files
Other Useful Links
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.
Abecasis Group Meeting
2:30-4:00 p.m. on Fridays, room 2610, SPH I. Please note April 9, please use room 2690, SPH I.