create_snp_list_from_plink

# 9 October 2019
# The purpose of this code is to generate a SNP table. 
# Works, but SNP table is empty? Even though it uses the same data that generates PCA plots show genetic differentiation
# WD: /home/jkimball/haasx092/main_GBS/190910_samtools

# Make a bed file for use in writing the SNP list (next step)
plink --file myplink --allow-extra-chr --make-bed

# Make the SNP list
plink --bfile plink --maf 0.05 --geno 0.05 --allow-extra-chr --write-snplist