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.

CAVIAR was created by Farhad Hormozdiari, Emrah Kostem, Eun Yong Kang, Bogdan Pasaniuc and Eleazar Eskin

Manual

Online user's guide

Usage for one region:

Usage: ./CAVIAR [options] 

Options:
-h, --help            		show this help message and exit 
-o OUTFILE, --out=OUTFILE 	specify the output file
-l LDFILE, --ld_file=LDFILE the ld input file
-z ZFILE, --z_file=ZFILE	the z-score and rsID files
-r RHO, --rho-prob=RHO		set $pho$ probability 
-c causal			set the maximum number of causal SNPs
-f 1				to out the probaility of different number of causal SNP

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.

<---- myfile.Z ---->             
snp1   1.2
snp2   5.1
snp3   1.9
cnv1   -6.1
cnv2   -3.2
cnv3   -4

<- myfile.LD ->

1.000  0.840  0.050 0.050  0.001 -0.010
0.840  1.000  0.040 0.040 -0.010 -0.007
0.050  0.040  1.000 0.950  0.060 -0.001
0.050  0.040  0.950 1.000  0.06   0.003
0.001 -0.010  0.060 0.065  1.000  0.018
-0.01 -0.007 -0.001 0.003  0.018  1.000

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.

eCAVIAR was created by Farhad Hormozdiari, Ayellet V. Segre, Martijn van de Bunt, Xiao Li, Jong Wha J Joo, Michael Bilow, Jae Hoon Sul, Bogdan Pasaniuc and Eleazar Eskin

Manual

Online user's guide

Usage for one region:

Usage: ./eCAVIAR [options]

Options:
-h, --help                      show this help message and exit
-o OUTFILE, --out=OUTFILE       specify the output file
-l LDFILE, --ld_file=LDFILE 	the GWAS ld input file
-l LDFILE, --ld_file=LDFILE 	the eQTL ld input file
-z ZFILE, --z_file=ZFILE        the GWAS z-score and rsID files
-z ZFILE, --z_file=ZFILE        the eQTL z-score and rsID files
-r RHO, --rho-prob=RHO          set $pho$ probability
-c causal                       set the maximum number of causal SNPs
-f 1                            to out the probaility of different number of causal SNP