[BioC] VariantAnnotation ALT Field
Samuel Younkin
syounkin at jhsph.edu
Wed Nov 21 15:50:41 CET 2012
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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