Variant Annotation with R

library("VariantAnnotation")

## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## 
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## 
## The following object is masked from 'package:stats':
## 
##     xtabs
## 
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, as.vector, cbind,
##     colnames, do.call, duplicated, eval, evalq, Filter, Find, get,
##     intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rep.int, rownames, sapply, setdiff, sort,
##     table, tapply, union, unique, unlist
## 
## Loading required package: GenomicRanges
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
## Loading required package: Rsamtools
## Loading required package: XVector
## Loading required package: Biostrings
## 
## Attaching package: 'VariantAnnotation'
## 
## The following object is masked from 'package:base':
## 
##     tabulate

vcf <- readVcf("sample.vcf", "DmelX")

## Warning: Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': <X>
##   - in 'y': X
##   Make sure to always combine/compare objects based on the same reference
##   genome (use suppressWarnings() to suppress this warning).

head(vcf)

## class: CollapsedVCF 
## dim: 1 27 
## rowData(vcf):
##   GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
## info(vcf):
##   DataFrame with 2 columns: JP, JE
## info(header(vcf)):
##       Number Type  Description                         
##    JP 4      Float Allele frequencies returned by JGIL 
##    JE 4      Float Error probabilities returned by JGIL
## geno(vcf):
##   SimpleList of length 2: GT, GQ
## geno(header(vcf)):
##       Number Type    Description     
##    GT 1      String  Genotype        
##    GQ 1      Integer Genotype Quality

sessionInfo()

## R version 3.1.0 (2014-04-10)
## Platform: x86_64-apple-darwin10.8.0 (64-bit)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] VariantAnnotation_1.10.0 Rsamtools_1.16.0        
## [3] Biostrings_2.32.0        XVector_0.4.0           
## [5] GenomicRanges_1.16.2     GenomeInfoDb_1.0.2      
## [7] IRanges_1.22.5           BiocGenerics_0.10.0     
## [9] knitr_1.5               
## 
## loaded via a namespace (and not attached):
##  [1] AnnotationDbi_1.26.0    BatchJobs_1.2          
##  [3] BBmisc_1.6              Biobase_2.24.0         
##  [5] BiocParallel_0.6.0      biomaRt_2.20.0         
##  [7] bitops_1.0-6            brew_1.0-6             
##  [9] BSgenome_1.32.0         codetools_0.2-8        
## [11] DBI_0.2-7               digest_0.6.4           
## [13] evaluate_0.5.5          fail_1.2               
## [15] foreach_1.4.2           formatR_0.10           
## [17] GenomicAlignments_1.0.0 GenomicFeatures_1.16.0 
## [19] iterators_1.0.7         plyr_1.8.1             
## [21] Rcpp_0.11.1             RCurl_1.95-4.1         
## [23] RSQLite_0.11.4          rtracklayer_1.24.0     
## [25] sendmailR_1.1-2         stats4_3.1.0           
## [27] stringr_0.6.2           tools_3.1.0            
## [29] XML_3.98-1.1            zlibbioc_1.10.0