ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.918/0.919 on github), see Change_log for changes, and download it here.

Supersim

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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]