Extracting genotype data from 1000 genome project phase I by using rsID Remotely ?

Question

[Yean]

Hi all

I usually use Plink1.9 to deal with the genotype data for variant and individuals manipulation such as genotype extraction based on rsID locally in my laptop.

I am wondering that are there any methods that are able to extract genotype data of certain population based on multiple set of rsID remotely from 1000 genome project phase 1 dataset at once like plink1.9 can do it by using --extract flag?

As far as i know, the only method to that to use for loop in tabix to extract SNPs one by one based on genomic position and chromosome.

However, using for loop may take a long time if I have a large number of SNPs. So any suggestion to achieve this with more efiiciency ?.

Thanks

[GenoMax]

While you wait for an answer to your question, have you tried using a loop? The extraction using tabix is reasonably fast with a region (instead of one SNP).

[Yean]

To be honest, I did not try it yet.

I am just wondering if there are any methods to extract genotype based on rsID instead of a region remotely.

Or using tabix is the standard method (fastest !!!) when extracting genotype based on position remotely ?

If so, maybe it's worth that I will try to do it first.

Answer 1

[Shicheng Guo]

First to download 1000G data with tabix

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-39967768 > G1000.vcf

Then use bcftools to extract the information for the SNPs you want.

bcftools view -T SNP.bed G1000.vcf -Oz -o SNP.vcf.gz