[adegenet-forum] Convert VCF file into genlight

[Francesco Montinaro]

Dear linda,

vcftool is good option even if the software has a few bugs. Did you try to
use the --plink-tped option instead of --plink? Then you can use plink to
transform the tped file in raw plink file.

Moreover there is a tools in the 1000G Project website (
http://www.1000genomes.org/vcf-ped-converter) but honestly I never tried it.

Another option could be to use SNPrelate R package transforming your vcf
file in GDS using the function snpgdsVCF2GDS and then the snpgdsGDS2BED or
snpgdsGDS2PED function to transform your file in Plink format.

Hoping that these software could help you.

Best,

Francesco

On 12 December 2012 11:01, <
adegenet-forum-request at lists.r-forge.r-project.org> wrote:

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>    1. Re: Convert VCF file into genlight (Valeria Montano)
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>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 11 Dec 2012 12:00:15 +0100
> From: Valeria Montano <mirainoshojo at gmail.com>
> To: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
> Cc: "adegenet-forum at r-forge.wu-wien.ac.at"
>         <adegenet-forum at r-forge.wu-wien.ac.at>
> Subject: Re: [adegenet-forum] Convert VCF file into genlight
> Message-ID:
>         <CADEmh=
> uD1ZVSsbNy_uFX_9wwMhqq+PixGtVJ2Z6a5S-ocfDejw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello
>
> there is this bedtools <http://code.google.com/p/bedtools/> software that
> might help out. It can convert .vcf to .bed format and then form .bed to
> .fasta ...or also from .vcf to .bam, I know it only superficially though.
>
> These problems make me feel old.
>
> Ciao
>
> Valeria
>
> On 11 December 2012 11:25, Jombart, Thibaut <t.jombart at imperial.ac.uk
> >wrote:
>
> > Hi there,
> >
> > sorry, I'm useless here, I never used this format.
> >
> > Anyone out there may know?
> >
> > Cheers
> >
> > Thibaut
> > ________________________________________
> > From: Linda Rutledge [lrutledge at trentu.ca]
> > Sent: 10 December 2012 19:25
> > To: Jombart, Thibaut
> > Cc: adegenet-forum at r-forge.wu-wien.ac.at
> > Subject: Re: [adegenet-forum] Convert VCF file into genlight
> >
> > Hi
> >
> > I've been trying to convert to PLINK raw format but no luck so far. I've
> > tried vcftools, PLINK, rplinkseq, IGV, and am now trying GATK. Any
> > suggestions out there for converting VCF to PLINK raw (or into genlight
> > object for analysis in adegenet) appreciated.
> >
> > Linda
> >
> >
> > On 2012-12-10, at 6:27 AM, Jombart, Thibaut wrote:
> >
> > Hello,
> >
> > if you can use PLINK to convert VCF files to PLINK's raw format, then you
> > can use read.PLINK to generate a genlight.
> >
> > Cheers
> >
> > Thibaut
> > ________________________________________
> > From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
> > adegenet-forum-bounces at lists.r-forge.r-project.org> [
> > adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
> > adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Linda
> > Rutledge [lrutledge at trentu.ca<mailto:lrutledge at trentu.ca>]
> > Sent: 07 December 2012 18:32
> > To: adegenet-forum at r-forge.wu-wien.ac.at<mailto:
> > adegenet-forum at r-forge.wu-wien.ac.at>
> > Subject: [adegenet-forum] Convert VCF file into genlight
> >
> > Hi
> >
> > Is there an easy way to convert VCF files of SNPs into genlight format
> for
> > analysis with adegenet? Thanks.
> >
> >
> > _______________________________________________
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