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

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