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

Daniel Cameron [guest] guest at bioconductor.org
Fri Oct 25 05:58:43 CEST 2013


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        

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