From the Bush Lab and Haines Lab, Mariusz Butkiewicz has developed COCOS, a plugin for the Ensembl Variant Effect Predictor (VEP) plugin for annotating reading frame changes. The plugin captures Amino Acid sequence alterations stemming from variants that produce an altered reading frame, e.g. stop-lost variants and small genetic Insertion and Deletions (InDels). The GitHub repository for COCOS can be found here.
From the Bush Lab: This archive contains scripts and data for performing an analysis looking for cis-interacting variants that influence gene expression. Our publication can be found here: http://www.cell.com/ajhg/fulltext/S0002-9297(16)30323-8