How to obtain human genotype data from dpSNP ftp?
I want to obtain all.vcf from dbSNP ftp to human learn reference alleles. After download human9606 all.vcf, I want to convert bed file in plink.
plink --vcf All.vcf --extract snpids.txt --make-bed
But it gives following error
https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to plink.log.
15924 MB RAM detected; reserving 7962 MB for main workspace.
Error: No genotype data in .vcf file.
As far as I know, there should be genotype data in vcf file, what is the meaning of error?
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Give it a try with vcftools
http://vcftools.sourceforge.net/man_0112a.html