Re: [Vcftools-help] VCF.pm does not accespt lower case bases

[Petr D. <pd...@sa...>]

Hi Tim,

VCF 4.0 requires the bases are in uppercase, but in the version VCF 4.1
the bases are not case sensitive.

So either change your VCF file to be in uppercase (a trivial thing to
do) or change the header to read ##fileformat=VCFv4.1. Changing the
regex in Vcf.pm is not recommended, as other tools may rely on the
uppercase bases.

Best,
Petr


On Tue, 2011-04-05 at 17:49 +0100, Timothee Cezard wrote:
> Hi all,
> I ran into a problem today where merge-vcf was crashing on my file 
> saying it can't parse the genotype information.
> after looking into the code I figured that it comes from the fact that 
> only upper case bases are accepted in the regex.
> Is this part of the VCF specification?
> I changed the regex in the VCF 4.0 class definition so it doesn't crash 
> anymore but it's probably not the best way.
> 
> Tim
> 




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