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#how many raw genotyped sites to be have? vcftools --vcf raw_calls.vcf #After filtering, kept 4 out of 4 Individuals #After filtering, kept 14559 out of a possible 14559 Sites #now perform basic quality filtering on raw calls bcftools filter --exclude 'QUAL < 30' raw_calls.vcf | bcftools view > filt0.vcf #check the new quality checked vcf vcftools --vcf filt0.vcf #Additionally, you can filter on representation among samples, allele frequency, and other options with VCFtools #Filter for biallelic sites variants #genotyped in 75% of samples, #with at least two reads covering the site vcftools --vcf filt0.vcf --max-alleles 2 --max-missing 0.75 --minDP 2 --recode --out filt2 |
Complete.