Extracting Specific Snps From 1K Genomes Database

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10.7 years ago

Carl ▴ 40

Hi everyone, my goal is to download a set of SNPs (around 100) located across the genome from the 1K Genome Database. I would like to use tabix and then Vcftools to convert this file in a PED/MAP format, in order to do the analyses with PLINK. The problem is that I don't know any script which will allow me to download these SNPs.

Anyone could help? I would appreciate your help. Cheers.

snps vcftools 1000genomes tabix • 2.4k views

ADD COMMENT • link 10.7 years ago by Carl ▴ 40

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I would recommend you to download all the 1000Genomes files in local, and then use the --snps option of vcftools to extract all the IDs. Tabix sometimes gives some silent download errors, and you risk to miss some data in the process. If you install the aspera client, you can download all the 1000Genomes data in half an hour.

ADD REPLY • link 10.7 years ago by Giovanni M Dall'Olio 28k

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