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I figured out, and tried to delete the post, but no option for deleting.

The answer is: rowRanges(all)@elementMetadata has all information on the right hand side of bar separation.

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If I load a vcf file, and go to rowRanges slot:

> rowRanges(all)[2:5]

GRanges object with 4 ranges and 5 metadata columns:
              seqnames         ranges strand | paramRangeID            REF
                 <Rle>      <IRanges>  <Rle> |     <factor> <DNAStringSet>
  1:12783_G/A        1 [12783, 12783]      * |         <NA>              G
  1:13110_G/A        1 [13110, 13110]      * |         <NA>              G
  1:13116_T/G        1 [13116, 13116]      * |         <NA>              T
  1:13118_A/G        1 [13118, 13118]      * |         <NA>              A
                             ALT      QUAL      FILTER
              <DNAStringSetList> <numeric> <character>
  1:12783_G/A                  A     33.56           .
  1:13110_G/A                  A    103.15           .
  1:13116_T/G                  G   1681.37           .
  1:13118_A/G                  G   1591.21           .

  I would like to take the values in the slot "REF", but in fact, this is not a slot:

> getClass(class(all@rowRanges))
Class "GRanges" [package "GenomicRanges"]

Slots:

Name:         seqnames          ranges          strand elementMetadata
Class:             Rle         IRanges             Rle       DataFrame

Name:          seqinfo        metadata
Class:         Seqinfo            list

I can get the information with names(rowRanges(all)), but some names in this vector are already translated to "rs" numbers.

So I still need to get values for the columns REF and ALT. How?

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE 13.1 (Bottle) (x86_64)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] VariantAnnotation_1.20.3   Rsamtools_1.26.2
 [3] Biostrings_2.42.1          XVector_0.14.1
 [5] SummarizedExperiment_1.4.0 Biobase_2.34.0
 [7] GenomicRanges_1.26.4       GenomeInfoDb_1.10.3
 [9] IRanges_2.8.2              S4Vectors_0.12.2
[11] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10             AnnotationDbi_1.36.2     GenomicAlignments_1.10.1
 [4] zlibbioc_1.20.0          BiocParallel_1.8.2       BSgenome_1.42.0
 [7] lattice_0.20-35          tools_3.3.3              grid_3.3.3
[10] DBI_0.6-1                digest_0.6.12            Matrix_1.2-8
[13] rtracklayer_1.34.2       bitops_1.0-6             biomaRt_2.30.0
[16] RCurl_1.95-4.8           memoise_1.1.0            RSQLite_1.1-2
[19] GenomicFeatures_1.26.4   XML_3.98-1.6

Don't use slot access, but instead use accessors. After running

example(readVcf)

there's an object vcf. I can access rowRanges(vcf), which is a 'GRanges' object. From the help page ?GRanges I find that I can access

mcols(rowRanges(vcf))

to retrieve a DataFrame, and then

mcols(rowRanges(vcf))$REF

or (also from ?GRanges) simply

rowRanges(vcf)$REF

From the main VariantAnnotation vignette or the help page ?VCF, I see that there's also a direct accessor

ref(vcf)