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 > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
