Converting VCF to PLINK PED format, need help?

ketan_bnf

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Join Date: Oct 2010

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#1

Converting VCF to PLINK PED format, need help?

02-21-2011, 10:16 PM

Hi all,

I want to convert my vcf file to PLINK PED format for input to WGAViewer.

vcftools --vcf my.vcf --plink gives *.ped and *.map

I am attaching my ped file with this mail. When i put ped file in WGAViewer to convert it to *.wr format it says SNP and p value cannot be the same. Why?

Is there any other tool to transform vcf to plink format.

Thanks
Attached Files

chr2.txt (7.0 KB, 221 views)
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rajeshkmaurya08

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Join Date: Feb 2017

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#2

03-13-2017, 10:59 PM

Actually i would like to know how you running this command.
For me it is showing Unknown option.
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olavur

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Join Date: Mar 2017

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#3

03-21-2017, 01:35 AM

This is the correct way to convert VCF to the Plink PED format using VCFtools. Your problem lies elsewhere (I can't help you with WGAViewer, unfortunately).
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