Performing population stratification based on GWA tutorial

Performing population stratification based on GWA tutorial

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Hi, I’m performing QC steps of Andries T. Marees GWA tutorial, currently I’m stuck at 7th step where you should begin the population stratification downloading a 61GB vcf.gz file of 1000genomes containing genetic data of 629 individuals from different ethnic backgrounds. Successively variants should be extracted with PLINK to obtain bim-fam-bed files.

wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz

During the extraction process I learn the file is corrupted; I tried to unzip it as well but with no success. I tried to download it 4 times but it is always corrupted. Has someone found the same issue?

Tutorial: github.com/MareesAT/GWA_tutorial

Article: www.ncbi.nlm.nih.gov/pmc/articles/PMC6001694/

Error


gwas


gwa


populationstratification


plink

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