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titlequality filter variants
#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