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[[Examples|Examples]] - Sample command lines with discussion
 
[[Examples|Examples]] - Sample command lines with discussion
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[[MapabilityScores]] - Definitions of various mappability scores adopted at UCSC genome browser.
  
 
=== Variant Calling ===
 
=== Variant Calling ===

Revision as of 23:21, 17 March 2010

Abecasis Group Wiki


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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

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.

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

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.

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