Re: [Samtools-help] how to analyze vcf version 4.1 generated by mpileup and bcftools

[Heng Li <lh...@sa...>]

Samtools takes the GL/PL ordering required by the upcoming VCF-4.1. Thus it labels 4.1 in the header. However, the release of VCF-4.1 is delayed, which is causing the inconsistency. For now, you may just replace "VCFv4.1" with "VCFv4.0". This will have no side effect for both samtools and the current version of vcftools.

Heng

On Apr 7, 2011, at 4:36 PM, Cliff Yiu wrote:

> Hi,
> 
> I used samtools mpileup and bcftools to get variant vcf files and noticed the vcf format is 4.1. I then tried vcftools to analyze the data but got the following  error message:
> 
> 
> VCFtools - v0.1.3
> (C) Adam Auton 2009
> 
> Error:VCF version must be v4.0:
> You are using version VCFv4.1
> 
> Is there any tool that I can use for vcf4.1?
> 
> Thanks
> 
> -C
> 
> 
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