Why does deepvariant make a call if the allele does not exist in the sample?

Question

[Frieda]

Hello,

Using WES model, deepvariant calls the following variant in the vcf file:

NC_000001.11    84574341    .   CAGCAGCGCT  C,T .   .   .   GT:GQ:DP:AD:VAF:PL  1/0:3:97:25,45,26:0.463918,0.268041:36,0,47,0,16,44

For this variant, the genotype is 1/0, meaning that one allele is REF, and the other allele is C. What is confusing is that deepvariant also calls a T however this is not referenced anywhere in the GT field.

What is the point of calling T if it does not occur in the sample?

Answer 1

[Pierre Lindenbaum]

What is the point of calling T if it does not occur in the sample?

the genotype was called as 0/1 = CAGCAGCGCT/ C

but if you look at the FORMAT/AD field you'll see that the genotype is quite dirty (GQ is low); At this position there is the following count of bases:

25 CAGCAGCGCT
45 C
26 T