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Welcome to the Variant Association Tools (VAT) tutorial session at ISMB 2018

(c) 2018 Gao Wang and Suzanne Leal

To run the live demo as I'll be doing at the tutorial session, you need two software packages:

  1. SoS Notebook
  2. docker

Notice that to gaurantee the best learning experience, our software tool, VAT, is pre-installed to a docker image we'd like to use for the tutorial session, although you are also welcome to follow VAT documentation and install VAT locally on your computer.

Reference

Rare variant data processing, association tools, and the ESP application

  1. F. Anthony San Lucas, Gao Wang, Paul Scheet, and Bo Peng (2012) Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools, Bioinformatics 28 (3): 421-422.
  2. Gao Wang, Bo Peng and Suzanne M. Leal (2014) Variant Association Tools for Quality Control and Analysis of Large-Scale Sequence and Genotyping Array Data, The American Journal of Human Genetics 94 (5): 770–83.
  3. Auer PL et al (2016) Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project, Am J Hum Genet. 99 (4): 791-801.

Other application examples

  1. Fuchsberger C et al, The genetic architecture of type 2 diabetes. Nature. 2016 Aug 4;536(7614):41-47. doi: 10.1038/nature18642.
  2. Mahajan A et al, Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes. Nat Genet. 2018 Apr;50(4):559-571. doi: 10.1038/s41588-018-0084-1.
  3. Mahajan A et al, Fine-mapping of an expanded set of type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps, biorxiv. doi: 10.1101/245506
  4. Werling DM et al, An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat Genet. 2018 May;50(5):727-736. doi: 10.1038/s41588-018-0107-y.