ERVCaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data.

http://www.uvm.edu/genomics/software/ERVcaller.html

ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data