[Bioc-devel] VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry

[Julian Gehring]

Dear Valerie,

The 'hgvs' fields seems to break the import, so having the '
--hgvs' (or another option including this) are definitely required.

I have sent you a minimal VCF file and code to reproduce this via 
e-mail.  If you need more, please let me know.

Best wishes
Julian


On 02/27/2013 08:53 PM, Valerie Obenchain wrote:
> Julian,
>
> I'm trying to produce a vcf file with these premature endings for
> testing but am having no luck. Can you send me a small example of a vcf
> with the premature ends? Or maybe there is a combination of VEP flags
> that often result in this case?
>
> Thanks,
> Valerie
>
>
> On 02/26/13 09:50, Julian Gehring wrote:
>> Hi,
>>
>> I tried to use the latest devel version of 'readVcf' to import a VCF
>> file with information from the ensembl VEP
>> (http://www.ensembl.org/info/docs/variation/vep/index.html).
>>
>> For a VCF entry with CSQ information like
>>
>> ""
>> 1    887899    .    A    G    .    .
>> NS=1;CSQ=G|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1134|1084|362|L|Ttg/Ctg||10/19||NOC2L|||||||YES||||ENSP00000317992||CCDS3.1|ENST00000327044.6:c.1084T>C|ENST00000327044.6:c.1084T>C(p.=)|
>> AR:RR:DP:AAP:RAP    2:14:16:1:1
>> ""
>>
>> the imported info field ends prematurely without any warning:
>>
>> ""
>> G|ENSG00000188976|ENST00000327044|Transcript|synonymous_variant|1134|1084|362|L|Ttg/Ctg||10/19||NOC2L|||||||YES||||ENSP00000317992||CCDS3.1|ENST00000327044.6:c.1084T>C|ENST00000327044.6:c.1084T>C(p.
>>
>> ""
>>
>> Versions:
>> R 2013-02-25 r62062
>> VariantAnnotation_1.5.39
>>
>>
>> Best wishes
>> Julian
>>
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>