I found that the genome build of the VcfFiles downloaded from AnnotationHub is obscure: the genome and tags fields mismatch as shown below.
> library(AnnotationHub)
> ah <- AnnotationHub() > vfs <- query(ah, 'VcfFile') > mcols(vfs)[, c(1,5,7)]
DataFrame with 8 rows and 3 columns title genome tags <character> <character> <character> AH50420 clinvar_20160203.vcf.gz hg19 dbSNP, GRCh37, VCF AH50421 clinvar_20160203_papu.vcf.gz hg19 dbSNP, GRCh38, VCF AH50422 common_and_clinical_20160203.vcf.gz hg19 dbSNP, GRCh37, VCF AH50423 common_no_known_medical_impact_20160203.vcf.gz hg19 dbSNP, GRCh38, VCF AH50424 clinvar_20160203.vcf.gz hg19 dbSNP, GRCh37, VCF AH50425 clinvar_20160203_papu.vcf.gz hg19 dbSNP, GRCh38, VCF AH50426 common_and_clinical_20160203.vcf.gz hg19 dbSNP, GRCh37, VCF AH50427 common_no_known_medical_impact_20160203.vcf.gz hg19 dbSNP, GRCh38, VCF
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale: [1] LC_CTYPE=ko_KR.UTF-8 LC_NUMERIC=C LC_TIME=ko_KR.UTF-8 LC_COLLATE=ko_KR.UTF-8 LC_MONETARY=ko_KR.UTF-8 LC_MESSAGES=ko_KR.UTF-8 [7] LC_PAPER=ko_KR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.16.4 Rsamtools_1.22.0 Biostrings_2.38.4 XVector_0.10.0 SummarizedExperiment_1.0.2 GenomicRanges_1.22.4 [7] GenomeInfoDb_1.6.3 AnnotationHub_2.2.5 org.Hs.eg.db_3.2.3 RSQLite_1.0.0 DBI_0.3.1 AnnotationDbi_1.32.3 [13] IRanges_2.4.8 S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1 loaded via a namespace (and not attached): [1] Rcpp_0.12.4 BiocInstaller_1.20.1 futile.logger_1.4.1 GenomicFeatures_1.22.13 bitops_1.0-6 [6] futile.options_1.0.0 tools_3.2.3 zlibbioc_1.16.0 biomaRt_2.26.1 digest_0.6.9 [11] BSgenome_1.38.0 shiny_0.13.2 curl_0.9.7 rtracklayer_1.30.4 httr_1.1.0 [16] R6_2.1.2 XML_3.98-1.4 BiocParallel_1.4.3 lambda.r_1.1.7 codetools_0.2-14 [21] GenomicAlignments_1.6.3 htmltools_0.3.5 mime_0.4 interactiveDisplayBase_1.8.0 xtable_1.8-2 [26] httpuv_1.3.3 RCurl_1.95-4.8