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.
Nielsen2012
Rasmus Nielsen, Thorfinn Korneliussen, Anders Albrechtsen, Yingrui Li1, Jun Wang, SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data. PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0037558