Hi! I realized my genome assembly de novo in STACKS and I used this command to called the SNPs in VCF format.
populations -P ../stacks -M ../stacks/popmap.lst --fstats --vcf --genepop --threads 80
I have a problem with the VCF, I don´t have any value of quality (column "QUAL"), I don´t know what´s wrong.
Thank you so much! and please feel free to ask me any additional info.