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 Korneliussen3, Anders Albrechtsen3, Yingrui Li1, Jun Wang, SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data