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

[Valerie Obenchain]

No problem. Glad it works for you.

Valerie

On 11/05/13 20:31, Daniel Cameron wrote:
> Works with R 3.0.2 / VariationAnnotation 1.8.2 for both minimal test
> case and my actual data. Sincere apologies for the inconvenience caused.
>
> Regards
> Daniel Cameron
>
> On 6/11/2013 11:25 AM, Valerie Obenchain wrote:
>> 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.
>>>
>>
>
>
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