Re: [Vcftools-help] VCF-Annotate

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

Hi Mario,

the command line does not seem correct. Did you mean -f d=4/-D ? 

Petr

On Wed, 2011-11-23 at 13:16 +0100, Mario Deng wrote:
> Hello everyone,
> 
> at the moment I am trying to use the vcf-annotate command. I call it like this
> 
> zcat Normal5.vcf.gz | vcf-annotate -f d=4/D  | bgzip -c > Normal5_filtere.vcf.gz 
> 
> But then I get an error like this:
> 
> Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 27.
> Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 28.
> Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 29.
> Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 30.
> Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 31.
> Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 32.
> Use of uninitialized value in numeric lt (<) at /media/spare/software/vcftools_0.1.7/bin/vcf-annotate line 685, <STDIN> line 33
> ...
> 
> It doesn't matter which files I input. The input is generated by GATK.
> Also I don't get errors or warnings while compiling VCF-Tools. Every other command works fine, also the PERL Path is exported.
> 
> When I run the validator, I don't get error.
> 
> Any ideas?
> 
> With best,
> 
> Mario
> __
> md
> mar...@go...
> 
> 
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