Allele-specific call confidence normalized by depth of sample reads supporting the allele (AS_QD)

Category Variant Annotations

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Overview

Allele-specific call confidence normalized by depth of sample reads supporting the allele

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

Note that currently, when HaplotypeCaller is run with `-ERC GVCF`, the QD calculation is invoked before AD itself has been calculated, due to a technical constraint. In that case, HaplotypeCaller uses the number of overlapping reads from the haplotype likelihood calculation in place of AD to calculate QD, which generally yields a very similar number. This does not cause any measurable problems, but can cause some confusion since the number may be slightly different than what you would expect to get if you did the calculation manually. For that reason, this behavior will be modified in an upcoming version.

Caveat

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

Related annotations

• AS_QualByDepth outputs a version of this annotation that includes all alternate alleles in a single calculation.
• 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 4.1.7.0-SNAPSHOT built at Fri, 24 Apr 2020 12:01:12 -0400.