[adegenet-forum] Convert VCF file into genlight

[Jombart, Thibaut]

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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