CAVIAR/eCAVIAR

Installation

It is now hosted at GitHub and the installation is straightforward.

git clone https://github.com/fhormoz/caviar.git
cd caviar/CAVIAR-C++
make
 

Testing

Based on sample_data/ we can run through the following script,

CAVIAR -l sample_data/50_LD.txt -z CAVIAR-C++/sample_data/50_Z.txt -o 50
CAVIAR -l sample_data/DDB1.top100.sig.SNPs.ld -z CAVIAR-C++/sample_data/DDB1.top100.sig.SNPs.ZScores -o 100
eCAVIAR -l sample_data/GWAS.ADGC.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld \
        -l sample_data/eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld \
        -z sample_data/GWAS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.Z.txt \
        -z eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.ILMN_1810712.NM_015313.1.ARHGEF12.Z.txt \
        -o 75
 

References

Hormozdiari, F., et al., Identifying Causal Variants at Loci with Multiple Signals of Association. Genetics, 2014. 198(2): p. 497-508.

Hormozdiari, F., et al., Colocalization of GWAS and eQTL Signals Detects Target Genes. Am J Hum Genet, 2016. 99(6): p. 1245-1260.