Converting VCF to PLINK PED format, need help?

[ketan_bnf]

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

[rajeshkmaurya08]

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

[olavur]

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).