initialize() {
	initializeSLiMOptions(nucleotideBased=T);
	length = initializeAncestralNucleotides("./fasta/hs37d5_chr5.fa");
	defineConstant("L", length);
	initializeMutationTypeNuc("m1", 0.5, "f", 0.0);
	initializeGenomicElementType("g1", m1, 1.0, mmJukesCantor(1e-7));
	initializeGenomicElement(g1, 0, L-1); 
	initializeRecombinationRate(1e-8);
} 
1 late() {
	sim.addSubpop("p1", 30);
	p1.genomes.readFromVCF("./GBR/GBR.chr5.30.recode.vcf", m1);
	p1.setSubpopulationSize(300);
	log = sim.createLogFile("./GBR/GBR.POP30/sim9.gen300.chr5.log",logInterval=1);
	log.addGeneration();
	log.addSubpopulationSize(p1);
	log.addCustomColumn("FreqA", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[0];");
	log.addCustomColumn("FreqC", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[1];");
	log.addCustomColumn("FreqG", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[2];");
	log.addCustomColumn("FreqT", "nucleotideFrequencies(sim.chromosome.ancestralNucleotides())[3];");
} 
1:300 late() {
	mut = sim.mutationsOfType(m1);
}
300 late() { 
	g = p1.sampleIndividuals(200).genomes;
	g.outputVCF("./GBR/GBR.POP30/sim9.gen300.chr5.vcf");}