I have annotated SNPs using GATK, and have observed that in many 1/1 SNP sites (homozygeous alternate) the whole read depth (stated in DP) are supporting the the alternate allele (as seen in the AD field), while the reference allele is supported by 0 reads. So how GATK called this ref allele if there is no reads supporting it.
Example:
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mohsamir2016 •
Sure, but n my case 1/1 the allel is different from the reference allele and it called it as T, for instance. So it needs reads in the sample to support that. Also i have seen for many of 0/1 genotype a read for the reference allele ?
So my understanding is that there should be sequenced reads (from ones sample) that support the two copy (allele) of the position. and the n of these reads is written in the field AD in VCF file. Also the field DP is the total read depth supporting that variant. Do you mean that because it is 1/1, so both copies is different from the reference and that is why the 0 in the AD is because no reads is saying that any of these copies at that position is similar to the reference?
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mohsamir2016 •
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I've removed irrelevant tags from your post.
it didn't call it reference. it called it hom_alt. where in your figure do you think it called it reference?