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.