How to obtain human genotype data from dpSNP ftp?
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Entering edit mode
6.5 years ago
gulcek ▴ 20

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 follwing 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 gentype data in vcf file, what is thye meaning of error?

dbsnp vcf genotype plink • 1.9k views
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Entering edit mode

Give it a try with vcftools

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

 

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Entering edit mode
6.3 years ago
Adam ★ 1.0k

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

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