Also, Val has added in bioc-devel the ExpandedVCF class which is like the
old VCF, except one row per position+alt, so that there is a single ALT per
row, and positions can occur multiple times, one for each ALT. This
simplifies the DNAStringSetList column to a DNAStringSet, which is much
easier to manipulate.

Michael


On Wed, Nov 21, 2012 at 9:19 AM, Paul Shannon <pshannon@fhcrc.org> wrote:

> Hi Sam,
>
> Here's a quick workaround:
>
>   fixed(vcf)[ , c("REF", "ALT")]
>
> The backstory on this is that the ALT field is a DNAStringSetList which,
> until very recently (the change is in bioc-devel) displayed itself, via its
> show methods, as '######'.  Realizing this was somewhat less than helpful,
> the latest version of VariantAnnotation display the alt sequence in a more
> natural way.
>
> But in the meantime, and if you do not use bioc devel, the explicit
> extraction of REF and ALT demonstrated above should get you part of what
> you want.
>
>  - Paul
>
>
> On Nov 21, 2012, at 6:50 AM, Samuel Younkin wrote:
>
> > 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
> > >
> >
> > _______________________________________________
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> > Bioconductor@r-project.org
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> > Search the archives:
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>
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