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

[Vince F. <for...@gm...>]

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