As a heads up, the behavior of the ref(), alt(), qual() and filt() accessors have changed in the devel version of VariantAnnotation. Now instead of values(fixed(vcf))[["ALT"]])) you can simply alt(vcf) This now returns the single value instead of a GRanges with the value as an elementMetadata column. Hopefully this makes getting at these data easier. Valerie On 09/28/2012 07:44 AM, James W. MacDonald wrote: > Hi Mark, > > On 9/28/2012 6:06 AM, Mark Dunning wrote: >> Hi all, >> >> I am doing some processing of vcf files using the VariantAnnotation >> package, and eventually I want to write out a table that I can use the >> annovar annotation package tool on >> (http://www.openbioinformatics.org/annovar/). The table needs to be in >> the form >> >> CHR, Start, end, Ref, Alt >> >> e.g. >> >> 1 55 55 T G >> 1 2646 2646 G A >> >> I'm fine extracting the chromosome, start and end. To get the >> referrence alleles I do. >> >>> Ref<- as.data.frame(values(ref(vcf))[["REF"]])[,1] >> But the Alt allele is a bit more complicated. If I do something like; >> >>> alternate = as.data.frame(unlist(values(fixed(vcf))[["ALT"]]))[,1] > > How about > > alternate <- sapply(values(fixed(vcf))[["ALT"]], paste, collapse = ",") > > Best, > > Jim > > >> The number of rows could be greater than the number of variants in the >> vcf file, especially for indels where more than one alternate allele >> could be found. I can no longer easily construct the data frame. >> >> Is there an easy way to write all alternate alleles for the same >> position in a comma-separated string so that entries in the table >> could be in the form >> >> 1 55 55 T G,C >> (e,g, G and C alternate alleles were found for the SNP at position >> chromosome 1: 55-55) >> >> >> Regards, >> >> Mark >> >> >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] VariantAnnotation_1.2.11 Rsamtools_1.8.6 Biostrings_2.24.1 >> [4] ggplot2_0.9.2.1 GenomicRanges_1.8.13 IRanges_1.14.4 >> [7] BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.18.3 Biobase_2.16.0 biomaRt_2.12.0 >> [4] bitops_1.0-4.1 BSgenome_1.24.0 colorspace_1.1-1 >> [7] DBI_0.2-5 dichromat_1.2-4 digest_0.5.2 >> [10] GenomicFeatures_1.8.3 grid_2.15.1 gtable_0.1.1 >> [13] labeling_0.1 lattice_0.20-10 MASS_7.3-21 >> [16] Matrix_1.0-9 memoise_0.1 munsell_0.4 >> [19] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 >> [22] RCurl_1.91-1 reshape2_1.2.1 RSQLite_0.11.2 >> [25] rtracklayer_1.16.3 scales_0.2.2 snpStats_1.6.0 >> [28] splines_2.15.1 stats4_2.15.1 stringr_0.6.1 >> [31] survival_2.36-14 tools_2.15.1 XML_3.9-4 >> [34] zlibbioc_1.2.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >