VCFtools quality filtering

VCFtools provide a wide range of functionality for the filtering, analysis and transformation of vcf files. Typically, SNPs of quality < 20 and read depth < 20 are filtered out as they are considered low quality SNP calls. This can be done in VCFtools by using vcf-annotate command as follows:

cat file.vcf | vcf-annotate --filter Qual=20/MinDP=20 > file-filtered.vcf