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.
Plink
From version 0.549 we now support plink output files. Currently we only support the transposed .tfam/.tped files. But we are working on a native .bed/.bim/.fam dumper.
This method is essentially a wrapper around the existing genotype caller, and all options for the genotype caller can therefore be used for the plink formated output file.