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

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