Variant confidence normalized by unfiltered depth of variant samples (QD)

Category Variant Annotations

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Overview

Variant confidence normalized by unfiltered depth of variant samples

This annotation puts the variant confidence QUAL score into perspective by normalizing for the amount of coverage available. Because each read contributes a little to the QUAL score, variants in regions with deep coverage can have artificially inflated QUAL scores, giving the impression that the call is supported by more evidence than it really is. To compensate for this, we normalize the variant confidence by depth, which gives us a more objective picture of how well supported the call is.

Statistical notes

The QD is the QUAL score normalized by allele depth (AD) for a variant. For a single sample, the HaplotypeCaller calculates the QD by taking QUAL/AD. For multiple samples, HaplotypeCaller and GenotypeGVCFs calculate the QD by taking QUAL/AD of samples with a non hom-ref genotype call. The reason we leave out the samples with a hom-ref call is to not penalize the QUAL for the other samples with the variant call.

Here is a single sample example:

2	37629	.	C	G	1063.77	.	AC=2;AF=1.00;AN=2;DP=31;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.50;QD=34.32;SOR=2.376	GT:AD:DP:GQ:PL:QSS	1/1:0,31:31:93:1092,93,0:0,960

QUAL/AD = 1063.77/31 = 34.32 = QD

Here is a multi-sample example:

10	8046	.	C	T	4107.13	.	AC=1;AF=0.167;AN=6;BaseQRankSum=-3.717;DP=1063;FS=1.616;MLEAC=1;MLEAF=0.167;QD=11.54
   GT:AD:DP:GQ:PL:QSS	0/0:369,4:373:99:0,1007,12207:10548,98	    0/0:331,1:332:99:0,967,11125:9576,27	    0/1:192,164:356:99:4138,0,5291:5501,4505

QUAL/AD = 4107.13/356 = 11.54 = QD

Caveat

This annotation can only be calculated for sites for which at least one sample was genotyped as carrying a variant allele.

Related annotations

• Coverage gives the filtered depth of coverage for each sample and the unfiltered depth across all samples.
• DepthPerAlleleBySample calculates depth of coverage for each allele per sample (AD).

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GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.