QUAL, QD, and GQ
In single sample VCF and gVCF, the QUAL follows the definition of the VCF specification. For more information on the VCF specification, see the most current VCF documentation available on samtools/hts-specs GitHub repository.
| • | QUAL is the Phred-scaled probability that the site has no variant and is computed as: |
QUAL = -10*log10 (posterior genotype probability of a homozygous-reference genotype (GT=0/0))
That is, QUAL = GP (GT=0/0), where GP is the posterior genotype probability in Phred scale.
QUAL = 20 means there is 99% probability that there is a variant at the site. The GP values are also given in Phred-scaled in the VCF file.
| • | GQ is the Phred-scaled probability that the call is incorrect. |
GQ=-10*log10(p), where p is the probability that the call is incorrect.
GQ=-10*log10(sum(10.^(-GP(i)/10))) where the sum is taken over the GT that did not win.
GQ of 3 indicates a 50 percent chance that the call is incorrect, and GQ of 20 indicates a 1 percent chance that the call is incorrect.
| • | QD is the QUAL normalized by the read depth, DP. |
The formulation is summarized in the following table.
|
Metric |
QUAL |
GQ |
QD |
|
Description |
Probability that the site has no variant |
Probability that the call is incorrect |
Qual normalized by Depth |
|
Formulation |
QUAL = GP(GT=0/0) |
GQ=-10*log10(p) |
QUAL/DP |
|
Scale |
Unsigned Phred |
Unsigned Phred |
Unsigned Phred |
|
Numerical example |
QUAL=20: 1 % chance that there is no variant at the site QUAL=50: 1 in 1e5 chance that there is no variant at the site |
GQ=3, 50% chance that the call is incorrect GQ=20, 1% chance that the call is incorrect |
|
