These are complementary fields that represent two important ways of
thinking about the depth of the data for this sample at this site.
AD is the unfiltered allele depth, i.e. the number of reads that support each of the reported alleles. All reads at the position
(including reads that did not pass the variant caller’s filters) are
included in this number, except reads that were considered
uninformative. Reads are considered uninformative when they do not
provide enough statistical evidence to support one allele over
DP is the filtered depth, at the sample level. This gives you the number of filtered reads that support each of the reported alleles.
You can check the variant caller’s documentation to see which filters
are applied by default. Only reads that passed the variant caller’s
filters are included in this number. However, unlike the AD
calculation, uninformative reads are included in DP.
This post is so helpful.
My question is according to quality scoring of variants, the good AD threshold should be >8. Then how we can find our answer in VCF file as AD is written as 9,8?? @Casbon