[adegenet-forum] Convert VCF file into genlight

[Valeria Montano]

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.
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org<mailto:
> adegenet-forum at lists.r-forge.r-project.org>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20121211/9a1985f8/attachment.html>