Low GQX

Question

[sisalem]

I have a question about a GQX value of 15 for a variant. Should I discard this variant or accept it knowing that it passed QC metrics in Illumina variant interpreter?

Answer 1

[Kevin Blighe]

Please explain further what is being represented by the GQX flag. Information should be in the VCF header

[sisalem]

Thank you for your reply. This is the header of the VCF file:

GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}

[Kevin Blighe]

Thank you; so, it is just the minimum of the GQ of the variant or reference base at a given position. These should be measured on Phred scale, meaning that 15 equates to a 1 in 31.6 chance of being incorrect. The standard score is usually 30 (1 in 1000).

[sisalem]

Thank you for the explanation.