SCOPA - Software for COrrelated Phenotype Analysis
Genome-wide study-level multiple phenotype analysis, including dissection of association signals, has been implemented in SCOPA. The software requires specification of input genotype and sample files, and a list of phenotypes to be included in the analysis. SCOPA includes options to enable filtering on the basis of imputation quality, to output the variance-covariance matrix and phenotype effects (with standard errors) for each SNP, and to investigate association with all possible subsets of phenotypes using BIC.
Genome-wide meta-analysis has then been implemented in META-SCOPA. The software requires specification of a list of SCOPA output files representing studies to be included in the meta-analysis. META-SCOPA includes options to enable genomic control correction (at the study level and/or after meta-analysis), and filtering of SNPs on the basis of minor allele frequency (MAF) and imputation quality.