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.
LD
For estimation of LD based on genotype likelihoods you can use ngsLD
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.
For estimation of LD based on genotype likelihoods you can use ngsLD