I am trying to put together genotype and consequence information from a vcf file. I am using the VariantAnnotation package. I am not totally clear if there is a better way but this is what I am doing:

#Get consequence information
vcf <- readVcf(tempFile, genome="grc38")
csq <- data.frame(parseCSQToGRanges(vcf, VCFRowID=rownames(vcf)))

#get genotype information
genotypeInfo <- c("GT", "DP", "AD")
genotype <- geno(vcf)[,genotypeInfo]
genotype <- do.call(cbind,lapply(1:length(genotype), function(g) {
    x <- genotypeInfo[i]
    data.frame(genotype[[g]])
 }))
colnames(genotype) <- genotypeInfo

csq$id <- paste0(csq$CHROM,":",csq$POS,"_",csq$REF,"/",csq$ALT)
csq[,genotypeInfo] <- genotype[csq$id,]

I know this is not the best, in particular, problems come where there is more than one allele for the same reference (i.e. GT=1/2). In that case, what I see happening in my example is that not all the genotypes are defined in the geno(vcf) command. For example for

chr3 121476455 . TACAC TACACAC,T ...
GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL 1/2:76:19:36:2,10,9:2,10,9:0,0,0:PASS:237,91,77,105,0,108

Then the genotype appears as:

chr3:121476455_TACAC/TACACAC 1/2 NA 2, 10, 9

but the one corresponding to T/TACACAC does not appear anywhere. So I am wondering if I am making this too complicated?

Thank you in advance.