Post date: Nov 23, 2013 12:13:52 AM
I wan to run entropy on the melissa samples to look at population structure. To this end I first ran vcf2glWild.pl on varMelissaAll.vcf to grab make a genotype likelihood file for the non 'SELEXP' individuals. I also only retained loci with global maf > 5%. This yields 32913 loci which are in melissaWild.gl. I further want to subset this to roughly independent loci. I am in the process of writing a R script to do this (called sampleVariants.R, it is an the entropy directory within lycaeides_hostplants).