Re: [Vcftools-help] Error usinf vcf-merge

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

Hi Gil,

please try to run vcf-validator on the input files, is it possible
something is not quite right about them?

By the way, vcf-merge is not supported any more, I strongly recommend
using `bcftools merge` instead
http://samtools.github.io/bcftools/

Best wishes,
Petr


On Wed, 2017-03-01 at 17:20 +0200, Gil Stelzer wrote:
> Hi All
> 
> I used the following command - 
> vcf-merge S11_L001.freebayes.filtered.vcf.gz
> S11_L001.samtools.filtered.vcf.gz | bgzip -c > S11_L001.vcf.gz
> 
> I received the following error while using the
> 
> Using column name 'unknown' for
> S11_L001.freebayes.filtered.vcf.gz:unknown
> Using column name 'S11_L001.bam' for
> S11_L001.samtools.filtered.vcf.gz:S11_L001.bam
> Use of uninitialized value in hash element at
> /pipeline/exomeAnalysisPronto/seqtools/installed/vcftools0.1.13/perl/
> Vcf.pm line 1722, <$__ANONIO__> line 2.
> Use of uninitialized value in hash element at
> /pipeline/exomeAnalysisPronto/seqtools/installed/vcftools0.1.13/perl/
> Vcf.pm line 1722, <$__ANONIO__> line 5.
> Use of uninitialized value in hash element at
> /pipeline/exomeAnalysisPronto/seqtools/installed/vcftools0.1.13/perl/
> Vcf.pm line 1722, <$__ANONIO__> line 4.
> 
> This error message repeated itself many times
> Why is this happening and how should I treat this?
> 
> Many thanks
> Gil
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