Hi Julian,
Thanks for the bug report. I agree this situation should be handled. It
might be tomorrow before I get to this - I'll post back when it is done.
Valerie
On 02/26/2013 10:23 AM, Julian Gehring wrote:
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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
