Generally, in cancer variation studies, the variant allele fraction (VAF) is calculated using this formula: alt reads/total reads at the loci.
In a VCF file, the FORMAT/AD tag has two values, for ex., 43,45 where the numbers represent allelic depths for the ref and alt alleles for a sample in the order listed.
The FORMAT field also has the DP tag which is the total depth. The difference between AD and DP in short is that a ref or alt supporting reads gets counted towards AD only if it is informative. Whereas, in DP both informative and uninformative reads gets counted. More inf can be found here: https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD-is-lower-than-expected
My question iif it is possible that the total of alt reads and ref reads from the AD tag may not match the DP tag, what should be the best way to calculate VAF. Can I only focus on the AD tag and fo this calculation: alt reads/ref reads+alt reads, OR, is it okay to do this calculation- alt reads/DP