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<br> [[Image:2009.08 Group Retreat Photo.jpg|center|400px|Group Photo]]
We are developing [[Software|software tools]] for the analysis of next generation sequence data.
These tools include:
# Variant Calling with [[glfSingleGlfSingle]] and [[glfMultiplesGlfMultiples]]# Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]# Variant Annotations using [[vcfCodingSnpsVcfCodingSnps]]# Rare Variant Analysis using [[rvTestsRvTests]]# Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]# C++ APIs for sequence analsysis using [[C++ Library: libStatGen]]# Meta-analyze single variants or genes, including tools for generating summary statistics ([[rvtestsRvtests]]), annotating summary statistics ([[TabAnno]]), and performing meta-analysis (command line tool [[raremetalRaremetal]] and R package [[RareMETALS]]).
These tools and additional tools can be found on the [[Software]] page.
We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]
== High Level Tutorials ==
Some high-level tutorials on the analysis of next generation sequence data:
# [[Evaluating a Read Mapper on Simulated Data]]# [[SNP Call Set Properties]]# [[Generic Exome Analysis Plan]]
== Projects ==
[[SardiNIA]] - The SardiNIA longitudinal study of aging. [[1000 Genomes Project Pilot 1 SNP Calling]]
==Abecasis Group Meeting==
3:00-4:30 p.m. on Mondays, room 2610, SPH I.