Folder where files are: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/lycaeides_dubois/Variants
To do further analysis, we will focus on common (>5%) versus rare/less frequency (<5%) variants. So I decided to split my filtered vcf file into two files: lyc_commonvariants.gl and lyc_rarevariants.gl.
Usage:
perl vcf2gl_maf.pl 0.05 finalfilter_filtered_variantsLycaeides.vcf #outputs lyc_commonvariants.gl when maf >= 0.05 in the script and lyc_rarevariants when maf <= 0.05 in the script.
total number of variants = 39193 (
common variants (MAF > 5%) = 6652 (lyc_commonvariants.gl file)
low frequency variants (MAF < 5%) = 32541 (lyc_rarevariants.gl file)