[BioC] VariantAnnotation ALT Field

[Samuel Younkin]

I have been looking at the VariantAnnotation vignette and have 
encountered something strange.  The R code is below.  See how the ALT 
field lists only ########.  The vignette, however, correctly shows the 
alternate allele.  The data file chr22.vcf.gz also correctly contains 
the alternate allele information.

Any suggestions?

Thanks.

Sam

~~

 > library(VariantAnnotation)
 > fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
 > vcf <- readVcf(fl, "hg19")
 > head( fixed(vcf), 3 )
GRanges with 3 ranges and 5 metadata columns:
               seqnames               ranges strand | paramRangeID
                  <Rle>            <IRanges>  <Rle> |     <factor>
     rs7410291       22 [50300078, 50300078]      * |         <NA>
   rs147922003       22 [50300086, 50300086]      * |         <NA>
   rs114143073       22 [50300101, 50300101]      * |         <NA>
                          REF                ALT      QUAL      FILTER
               <DNAStringSet> <DNAStringSetList> <numeric> <character>
     rs7410291              A           ########       100        PASS 
 

   rs147922003              C           ########       100        PASS 
 

   rs114143073              G           ########       100        PASS 
 

   ---
   seqlengths:
    22
    NA
 > sessionInfo()
R version 2.15.2 Patched (2012-10-28 r61038)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
  [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
  [7] LC_PAPER=C                     LC_NAME=C
  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

other attached packages:
[1] VariantAnnotation_1.4.5 Rsamtools_1.10.2        Biostrings_2.26.2
[4] GenomicRanges_1.10.5    IRanges_1.16.4          BiocGenerics_0.4.0

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.20.3   Biobase_2.18.0         biomaRt_2.14.0
  [4] bitops_1.0-5           BSgenome_1.26.1        DBI_0.2-5
  [7] GenomicFeatures_1.10.1 parallel_2.15.2        RCurl_1.95-3
[10] RSQLite_0.11.2         rtracklayer_1.18.1     stats4_2.15.2
[13] tools_2.15.2           XML_3.95-0.1           zlibbioc_1.4.0
 >