Page Index - DianaCarolinaVergara/SNPs_pipeline GitHub Wiki 12 page(s) in this GitHub Wiki: Home Phylogeny Construction with SNPs Pipeline References 2. Packages and Files Needed 3. Extract SNPs and Indels 4. Quality Filtering 5. Write new VCFs 6. Minor Allele Frequency (MAF) 7. Convert vcf to genind 8. Graphics 9. Example Graphics