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Old 02-21-2011, 09:16 PM   #1
Location: India

Join Date: Oct 2010
Posts: 59
Default Converting VCF to PLINK PED format, need help?

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.

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File Type: txt chr2.txt (7.0 KB, 46 views)
ketan_bnf is offline   Reply With Quote
Old 03-13-2017, 10:59 PM   #2
Location: india

Join Date: Feb 2017
Posts: 14

Actually i would like to know how you running this command.
For me it is showing Unknown option.
rajeshkmaurya08 is offline   Reply With Quote
Old 03-21-2017, 01:35 AM   #3
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Location: Tˇrshavn, Faroe Islands

Join Date: Mar 2017
Posts: 2

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).
olavur is offline   Reply With Quote

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