How to obtain human genotype data from dpSNP ftp?

Question

[gulcek]

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?

[Floris Brenk]

Give it a try with vcftools

http://vcftools.sourceforge.net/man_0112a.html

Answer 1

[Adam]

The VCF files from dbSNP report only sites, not genotypes. To get genotyping data, perhaps you should use data from the 1000 Genomes Project?