Re: [Vcftools-help] IMPUTE2 to VCF while retaining dosage values

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

Hi Vince,

I see you already found a way. There is also this script which we
internally use in our pipelines
https://github.com/VertebrateResequencing/vr-codebase/blob/develop/scripts/vcf-impute2

It can convert between VCF and IMPUTE2 data, forth and back.

Best,
Petr



On Wed, 2012-10-17 at 16:21 -0400, Vince Forgetta wrote:
> qctool (http://www.well.ox.ac.uk/~gav/qctool/#overview) looks like the
> right tool.
> 
> On Tue, Oct 16, 2012 at 5:04 PM, Vince Forgetta <for...@gm...> wrote:
> > Hi,
> >
> > Is there a tool chain to convert IMPUTE2 data (.gen and .sample files)
> > to VCF format, while still retaining dosage values? For example, as a
> > GL formatted genotype.
> >
> > So far, I have come up with:
> >
> > 1. IMPUTE2 to PED using GTOOL
> > 2. PED to binary PED using PLINK
> > 3 .binaryPED to VCF using PLINKSEQ.
> >
> > But GTOOL thresholds the genotypes to integers.
> >
> > Thanks in advance for the help.
> >
> > Vince
> 
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