Hi Julian

I think your vcf file is off-spec. From the vcf spec at 
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

"INFO additional information: (String, no white-space, semi-colons, or 
equals-signs permitted;"

So that equals-sign in your INFO isn't allowed

HTH

Richard


On 26/02/2013 17:50, 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
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


	[[alternative HTML version deleted]]

