[BioC] Printing Alt alleles using VariantAnnotation

[Mark Dunning]

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]

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