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

[Valerie Obenchain]

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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