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

[Julian Gehring]

Hi Richard,

That is true that is not according to the specs.  However, the 
'ensemblVEP' package has the 'parseCSQToGRanges' method which extracts 
this kind of CSQ information from a 'VCF' object (as read in by 
'readVcf') and fails at the prematurely ended entries.  Perhaps having a 
VCF reader that tolerates this is useful.

Best wishes
Julian


On 02/26/2013 07:17 PM, Richard Pearson wrote:
> 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
>>
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>>
>