Methods

Colocalization (COLOC)

COLOC evaluates five hypotheses for a GWAS locus and a tissue eQTL. The one of interest is H4: a single shared causal variant drives both signals. PP.H4.abf is its posterior probability under the approximate Bayes factor model. A pair with PP.H4 ≥ 0.5 is called colocalized.

lncRNA co-expression

For each query lncRNA, expression is correlated against all genes across GTEx tissues (Pearson and Spearman, with partial correlations adjusting for tissue structure); high-correlation, low-adjusted-p partners are reported.

Reproducibility & performance

The full pipeline is open source and version-pinned at wanglab-upenn/inferno-containerized. Optimizations cut the advanced run from ~9.3 h to ~45 min (warm) while remaining byte-for-byte identical to the published reference.

Citation

Amlie-Wolf et al., INFERNO: inferring the molecular mechanisms of noncoding genetic variants, Nucleic Acids Research, 2018.