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