ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Li2010
Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, et al., 2010. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 42:969–972.