Record added by Jurg Ott (the original Rockefeller list)
UMAKE is a software pipeline to detect SNPs and call their genotypes from a list of BAM files. UMAKE pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies.
Goncalo Abecasis (Univ Michigan)
http://genome.sph.umich.edu/wiki/UMAKE