[BioC] readVcf fails when ALT field contains breakends and no symbolic allele

[Valerie Obenchain]

Hi Daniel,

I can't reproduce this error.

It looks like your version of R and Bioconductor packages are out of 
date. The current R version is 3.0.2 and VariantAnnotation is 1.8.2 
(release) and 1.9.7 (devel). Help for updating is here,

http://www.bioconductor.org/install/

Let me know if you get the same error after updating and send a small 
sample file if possible.

Thanks.
Valerie


On 10/24/2013 08:58 PM, Daniel Cameron [guest] wrote:
> readVcf fails to load VCF files where alternate alleles containing breakends exist but no symbolic alleles. If any variant in the VCF contains a symbolic alleles, then the VCF does load correctly (including any breakend alleles - see example below).
>
>
> Reproduction steps:
>> library(VariantAnnotation)
>> readVcf("fail.vcf", "fake.fa")
> Error in .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW),  :
>    key 91 (char '[') not in lookup table
>> readVcf("success.vcf", "fake.fa")
>
> fail.vcf:
> ##fileformat=VCFv4.1
> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
> ##ALT=<ID=DEL,Description="Deletion">
> #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
> 1	1	ref1	G	G[1:2[	.	PASS	SVTYPE=BND
>
> success.vcf:
> ##fileformat=VCFv4.1
> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
> ##ALT=<ID=DEL,Description="Deletion">
> #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
> 1	1	ref1	G	G[1:2[	.	PASS	SVTYPE=BND
> 1	2	ref2	G	<DEL>	.	PASS	SVTYPE=DEL
>
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] VariantAnnotation_1.4.12 Rsamtools_1.10.2         Biostrings_2.26.3        GenomicRanges_1.10.7     IRanges_1.16.6
> [6] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.20.7   Biobase_2.18.0         biomaRt_2.14.0         bitops_1.0-6           BSgenome_1.26.1
>   [6] DBI_0.2-7              GenomicFeatures_1.10.2 parallel_2.15.2        RCurl_1.95-4.1         RSQLite_0.11.4
> [11] rtracklayer_1.18.2     stats4_2.15.2          tools_2.15.2           XML_3.98-1.1           zlibbioc_1.4.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>