Re: [Vcftools-help] recode polyploid data

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

Hi Jan,

at the moment none of the scripts can do this but is easy to do using  
the perl API. I'll think about it later what would be a good general  
tool for tasks like this. Comments and suggestions welcome.

Best,
Petr



On Apr 13, 2011, at 12:18 PM, Uitdewilligen, Jan wrote:

> Can I filter out genotypes with the FORMAT:FT tag using the perl  
> scripts?
>
> Thanks, Jan
>
>
> From: Adam Auton [mailto:ada...@gm...]
> Sent: woensdag 13 april 2011 12:54
> To: Uitdewilligen, Jan
> Cc: vcf...@li...
> Subject: Re: [Vcftools-help] recode polyploid data
>
> I'm afraid that polyploidy isn't currently supported by the C++  
> module of VCFtools.
>
> Adam
>
> On 13 April 2011 11:51, Uitdewilligen, Jan  
> <jan...@wu...> wrote:
> Hi,
>
> When rewriting a VCF filtered file using --recode, tetraploid GT  
> fields (eg. 1/1/0/0/) get truncated to diploid calls (eg. 1/1). Can  
> you solve this?
>
> Thanks, Jan
>
> ------------------------------------------------------------------------------
> Forrester Wave Report - Recovery time is now measured in hours and  
> minutes
> not days. Key insights are discussed in the 2010 Forrester Wave  
> Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and  
> vision.
> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
> _______________________________________________
> Vcftools-help mailing list
> Vcf...@li...
> https://lists.sourceforge.net/lists/listinfo/vcftools-help
>
>
>
>
> -- 
> Adam Auton
> Post-Doctoral Research Scientist,
> Wellcome Trust Centre for Human Genetics,
> University of Oxford
> Roosevelt Drive
> Oxford
> OX3 7BN
> UK
> ------------------------------------------------------------------------------
> Forrester Wave Report - Recovery time is now measured in hours and  
> minutes
> not days. Key insights are discussed in the 2010 Forrester Wave  
> Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and  
> vision.
> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo_______________________________________________
> Vcftools-help mailing list
> Vcf...@li...
> https://lists.sourceforge.net/lists/listinfo/vcftools-help




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.