[Bioc-devel] VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry
julian.gehring at embl.de
Thu Feb 28 12:22:33 CET 2013
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.
On 02/27/2013 08:53 PM, Valerie Obenchain wrote:
> 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?
> On 02/26/13 09:50, Julian Gehring wrote:
>> I tried to use the latest devel version of 'readVcf' to import a VCF
>> file with information from the ensembl VEP
>> For a VCF entry with CSQ information like
>> 1 887899 . A G . .
>> AR:RR:DP:AAP:RAP 2:14:16:1:1
>> the imported info field ends prematurely without any warning:
>> R 2013-02-25 r62062
>> Best wishes
>> Bioc-devel at r-project.org mailing list
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