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 > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]