Depth and genotype quality in vcf file

Question

[ashaneev07]

Hello all,

If the depth is 15 and the genotype quality is below 50, could it still be a reliable variant in the VCF file? Additionally, if other variants have a depth above 50 and a genotype quality above 90, does that make them more likely to be true variants?

[KABILAN]

I think more sequencing depth and more quality score (i.e PHRED quality score) will indicate the true variant. Usually, PHRED quality scores above 30 are considered good basepairs, and an average sequencing depth of more than 10 is also considered good.