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.
MsToGlf
For the Korneliussen2013 paper, we simulated data according to genotypes simulated from ms/msms output. For this we used the msToGlf program found in the 'misc/' subfolder of the angsd tar ball.
Brief Overview
./msToGlf Probs with args, supply -in -out also -err -depth -depthFile -singleOut -regLen -nind