Re: [Vcftools-help] recode polyploid data

[Adam A. <ada...@gm...>]

I believe genotype-level filters can be applied regardless of ploidy.
However, I don't know if the perl module internally handles polypoildy
correctly. Petr?

Regards,
Adam

On 13 April 2011 12:18, Uitdewilligen, Jan <jan...@wu...> 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
>
>
>
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> --
> Adam Auton
> Post-Doctoral Research Scientist,
> Wellcome Trust Centre for Human Genetics,
> University of Oxford
> Roosevelt Drive
> Oxford
> OX3 7BN
> UK
>



-- 
Adam Auton
Post-Doctoral Research Scientist,
Wellcome Trust Centre for Human Genetics,
University of Oxford
Roosevelt Drive
Oxford
OX3 7BN
UK