ALoFT takes as input a VCF file or a five column tab-delineated variant file, runs it through the VAT tools snpMapper and indelMapper to annotate coding variants. ALoFT extracts putative LoF variant annotations from the VAT output and calculates variant-specific features that give functional, evolutionary, mismapping, and other information. ALoFT calculates these parameters for putative LoF variants defined as frameshift-causing indels, premature stop causing SNPs, and SNPs located in canonical splice sites.
You can find the source code on GitHub.