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

[Valerie Obenchain]

Thanks for sending the file. Now fixed in 0.99.14.

Valerie



On 02/28/2013 03:22 AM, Julian Gehring wrote:
> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>