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CAVIAR

CAVIAR (CAusal Variants Identication in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.

Manual

Online user’s guide

Usage for one region:

Input file format

CAVIAR requires two files to run. Z-score files and the pair-wise correlation, sign of corrleation is important .

In Z-score file, each line indicates one variants, its name and the z-score value computed from the marginal statistics.

In LD file, its a square matrix which indicates the pair-wise corrleation between pair of SNPs. We can obtain the LD matrix using the plink.

eCAVIAR

eCAVIAR (eQTL and GWAS CAusal Variants Identification in Associated Regions), a statistical framework that quantifies the probability of the variant to be causal both in GWAS and eQTL studies, while allowing with arbitrary number of causal variants. For each locus, eCAVIAR requires the summary statistics of all the variants in that locus from both the GWAS and eQTL. The eQTL summary staistics is for one gene in one tissue.

CAVIAR CAVIAR (CAusal Variants Identication in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of

CAVIAR

CAVIAR (CAusal Variants Identification in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.

eCAVIAR

eCAVIAR (eQTL and GWAS CAusal Variants Identification in Associated Regions), a statistical framework that quantifies the probability of the variant to be causal both in GWAS and eQTL studies, while allowing with arbitrary number of causal variants.

CHI3L2 Loci

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v2.0.0 (2017-08-06) A new version of CAVIAR/eCAVIAR was released.

v1.0.0 (2016-04-22) Preliminary version of eCAVIAR was deployed

v1.0.0 (2016-04-01) A faster version of CAVIAR was released.

v0.0.1 (2014-08-13) Our Paper got accepted!

v0.0.1 (2014-08-13) Preliminary version of CAVIAR was deployed

Publication

Farhad Hormozdiari, Ayellet V. Segre, Martijn van de Bunt, Xiao Li, Jong Wha J Joo, Michael Bilow, Jae Hoon Sul, Bogdan Pasaniuc and Eleazar Eski. Joint Fine Mapping of GWAS and eQTL Detects Target Gene and Relevant Tissue. The American Journal of Human Genetics (AJHG) , Read more.

Farhad Hormozdiari, Emrah Kostem, Eun Yong Kang, Bogdan Pasaniuc and Eleazar Eskin. Identifying Causal Variants at Loci with Multiple Signals of Association. Genetics, 44, 725–731 (2014). Read more.

CAVIAR CAVIAR (CAusal Variants Identification in Associated Regions), a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of