On Tue, Feb 26, 2013 at 1:23 PM, Julian Gehring <julian.gehr...@embl.de> 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.
And Ensembl is not being "arbitrary" in this: http://www.hgvs.org/mutnomen/recs-prot.html#silent Interesting how these standards work, isn't it.... > 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
