<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi<div><br></div><div>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.</div><div><br></div><div>Linda<div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><br></span>
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<br><div><div>On 2012-12-10, at 6:27 AM, Jombart, Thibaut wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello, <br><br>if you can use PLINK to convert VCF files to PLINK's raw format, then you 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">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Linda Rutledge [<a href="mailto:lrutledge@trentu.ca">lrutledge@trentu.ca</a>]<br>Sent: 07 December 2012 18:32<br>To: <a href="mailto:adegenet-forum@r-forge.wu-wien.ac.at">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 analysis with adegenet? Thanks.<br><br><br>_______________________________________________<br>adegenet-forum mailing list<br><a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br></div></blockquote></div><br></div></body></html>