Dear linda,<br><br>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.<br><br>Moreover there is a tools in the 1000G Project website (<a href="http://www.1000genomes.org/vcf-ped-converter" target="_blank">http://www.1000genomes.org/vcf-ped-converter</a>) but honestly I never tried it.<br>
<br>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.<br><br>
Hoping that these software could help you.<br><br>Best,<br><br>Francesco<br>
<br><div class="gmail_quote">On 12 December 2012 11:01, <span dir="ltr"><<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank">adegenet-forum-request@lists.r-forge.r-project.org</a>></span> wrote:<br>
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1. Re: Convert VCF file into genlight (Valeria Montano)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 11 Dec 2012 12:00:15 +0100<br>
From: Valeria Montano <<a href="mailto:mirainoshojo@gmail.com" target="_blank">mirainoshojo@gmail.com</a>><br>
To: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">t.jombart@imperial.ac.uk</a>><br>
Cc: "<a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at" target="_blank">adegenet-forum@r-forge.wu-wien.ac.at</a>"<br>
<<a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at" target="_blank">adegenet-forum@r-forge.wu-wien.ac.at</a>><br>
Subject: Re: [adegenet-forum] Convert VCF file into genlight<br>
Message-ID:<br>
<CADEmh=<a href="mailto:uD1ZVSsbNy_uFX_9wwMhqq%2BPixGtVJ2Z6a5S-ocfDejw@mail.gmail.com" target="_blank">uD1ZVSsbNy_uFX_9wwMhqq+PixGtVJ2Z6a5S-ocfDejw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello<br>
<br>
there is this bedtools <<a href="http://code.google.com/p/bedtools/" target="_blank">http://code.google.com/p/bedtools/</a>> software that<br>
might help out. It can convert .vcf to .bed format and then form .bed to<br>
.fasta ...or also from .vcf to .bam, I know it only superficially though.<br>
<br>
These problems make me feel old.<br>
<br>
Ciao<br>
<br>
Valeria<br>
<br>
On 11 December 2012 11:25, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">t.jombart@imperial.ac.uk</a>>wrote:<br>
<br>
> Hi there,<br>
><br>
> sorry, I'm useless here, I never used this format.<br>
><br>
> Anyone out there may know?<br>
><br>
> Cheers<br>
><br>
> Thibaut<br>
> ________________________________________<br>
> From: Linda Rutledge [<a href="mailto:lrutledge@trentu.ca" target="_blank">lrutledge@trentu.ca</a>]<br>
> Sent: 10 December 2012 19:25<br>
> To: Jombart, Thibaut<br>
> Cc: <a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at" target="_blank">adegenet-forum@r-forge.wu-wien.ac.at</a><br>
> Subject: Re: [adegenet-forum] Convert VCF file into genlight<br>
><br>
> Hi<br>
><br>
> I've been trying to convert to PLINK raw format but no luck so far. I've<br>
> tried vcftools, PLINK, rplinkseq, IGV, and am now trying GATK. Any<br>
> suggestions out there for converting VCF to PLINK raw (or into genlight<br>
> object for analysis in adegenet) appreciated.<br>
><br>
> Linda<br>
><br>
><br>
> On 2012-12-10, at 6:27 AM, Jombart, Thibaut wrote:<br>
><br>
> Hello,<br>
><br>
> if you can use PLINK to convert VCF files to PLINK's raw format, then you<br>
> can use read.PLINK to generate a genlight.<br>
><br>
> Cheers<br>
><br>
> Thibaut<br>
> ________________________________________<br>
> From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<br>
> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a>> [<br>
> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<br>
> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org" target="_blank">adegenet-forum-bounces@lists.r-forge.r-project.org</a>>] on behalf of Linda<br>
> Rutledge [<a href="mailto:lrutledge@trentu.ca" target="_blank">lrutledge@trentu.ca</a><mailto:<a href="mailto:lrutledge@trentu.ca" target="_blank">lrutledge@trentu.ca</a>>]<br>
> Sent: 07 December 2012 18:32<br>
> To: <a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at" target="_blank">adegenet-forum@r-forge.wu-wien.ac.at</a><mailto:<br>
> <a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at" target="_blank">adegenet-forum@r-forge.wu-wien.ac.at</a>><br>
> Subject: [adegenet-forum] Convert VCF file into genlight<br>
><br>
> Hi<br>
><br>
> Is there an easy way to convert VCF files of SNPs into genlight format for<br>
> analysis with adegenet? Thanks.<br>
><br>
><br>
> _______________________________________________<br>
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