[Bioc-devel] VariantAnnotation: 'readVcf' returns incomplete 'CSQ' entry
Dear Valerie, The 'hgvs' fields seems to break the import, so having the ' --hgvs' (or another option including this) are definitely required. I have sent you a minimal VCF file and code to reproduce this via e-mail. If you need more, please let me know. Best wishes Julian
On 02/27/2013 08:53 PM, Valerie Obenchain wrote:
Julian, I'm trying to produce a vcf file with these premature endings for testing but am having no luck. Can you send me a small example of a vcf with the premature ends? Or maybe there is a combination of VEP flags that often result in this case? Thanks, Valerie On 02/26/13 09:50, 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
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