Why my variant is found if AD alt = 0 in my vcf file ?

[Sam64]

Hi,

My problem is about intepretation of vcf file for indels variation, and particulary, about AD tag (Allele Depth) find in the last column. I obtained my vcf file after processing "Unified Genotyper / Hard filtering" method as recommended by GATK. And as you can read in my example, AD tag ==> 154,0 (DP=171). (AD tag means allelic depths for the ref and alt alleles in the order listed).

chr6 36485587 . GAATGTCACGCTCCGC G 760.73 PASS AC=1;AF=0.500;AN=2;DP=171;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;QD=0.30 GT:ADP:GQ:PL 0/1:154,0:171:99:798,0,25782

I don't understand how the variant can be detected if the AD Alt = 0 ?


Anybody could explain me please ?


Best,

Sam

[Sam64]

GATK forum

On GATK forum, you can read :

http://www.broadinstitute.org/gatk/g...eBySample.html

[...] Please note, however, that the AD isn't necessarily calculated exactly for indels. Only reads which are statistically favoring one allele over the other are counted. Because of this fact, the sum of AD may be different than the individual sample depth, especially when there are many non-informative reads.

Because the AD includes reads and bases that were filtered by the caller and in case of indels is based on a statistical computation, one should not base assumptions about the underlying genotype based on it; instead, the genotype likelihoods (PLs) are what determine the genotype calls.[...]

[Sam64]

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