[ensembl-dev] VCFtools parsing error in Ensembl Homo sapiens VCF files.

[Tjaart de Beer]

Hi,

I am trying to look for specific rsids in the latest release of human vcf
files from

ftp://ftp.ensembl.org/pub/release-73/variation/vcf/homo_sapiens/

I am using this file

Homo_sapiens_incl_consequences.vcf.gz

I installed the latest vcftools (0.1.11) and when I run the following command

vcftools --vcf Homo_sapiens_incl_consequences.vcf --snps test.dat

I get this error:

VCFtools - v0.1.11
(C) Adam Auton 2009

Parameters as interpreted:
        --vcf Homo_sapiens_incl_consequences.vcf
        --snps test.dat

Reading Index file.
Building new index file.
Error:Unknown Type in INFO meta-information:
##INFO=<ID=VE,Number=.,Type=ListOfString,Description="Effect that a
sequence alteration has on a sequence feature that overlaps
it.Format=SV|IDX|FT|FID">

According to the vcftools page, the only valid options for Type is
Integer, Float, Flag, Character, and String and not ListOfString

This thread from the vcftools mailing seems to support this that the
ListOfstring is an invalid option.

http://sourceforge.net/mailarchive/message.php?msg_id=31150267

Could this perhaps be a bug in the way the Ensembl vcf files are
generated? Or am I missing something?

--
Dr. Tjaart de Beer
Thornton group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom