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

[Julian Gehring]

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