ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.934/0.935 on github), see Change_log for changes, and download it here.

# Supersim

From angsd

Small program to simulate genotype likelihoods.

./supersim

./supersim -> Required arg: -outfiles PREFIX PREFIX.seq PREFIX.glf PREFIX.frq PREFIX.arg -> Optional arg: -npop Number of populations. This MUST be set before -nind [1] -nind Number of diploid individuals for each population [10] -nsites Number of sites [500000] -errate The sequencing error rate [0.0075] -depth Mean sequencing depth [5] -pvar Probability that a site is variable in the population [0.015] -mfreq Minimum population frequency [0.0001] -F inbreeding coefficient for each population [0] -model 0=fixed errate 1=variable errate [1] -simpleRand boolean [1] -base_freq Background allele frequencies for A,C,G,T [0.25 0.25 0.25 0.25]