#use vcftools to get information about our variant set
vcftools --vcf raw_calls.vcf
#returns this:
VCFtools - 0.1.15
(C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted:
--vcf raw_calls.vcf
After filtering, kept 3 out of 3 Individuals
After filtering, kept 14117 out of a possible 14117 Sites
#now quality filter the raw calls
bcftools filter --exclude 'QUAL < 30' raw_calls.vcf | bcftools view -g ^miss > qced_calls.vcf
#check the new quality checked vcf
vcftools --vcf qced_calls.vcf |