User: Opal

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Opal0
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Posts by Opal

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Comment: C: Where to find 1000 Genome phase 3 whole genome data and select only European pop
... Hi Kevin, I have downloaded the vcf.gz files for all the chromosomes 1-22 (I don't need X and Y). But they are pretty big files, is there any way to concatenate them without unzipping? Also, would you be able to elaborate how to use the .ped file to extract EUR (GBR, CEU, TSI, IBS, FIN) only popula ...
written 15 months ago by Opal0
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Comment: C: Where to find 1000 Genome phase 3 whole genome data and select only European pop
... Hi Kevin, I actually think the file >ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz is not the right file, because it says 'no sample in .vcf file. The naming of this file is also different from the other chromsome ...
written 15 months ago by Opal0
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Where to find 1000 Genome phase 3 whole genome data and select only European population
... Hello: I was trying to download whole genome data from 1000Genome phase 3 data and extract only the EUR population (GBR, TSI, FIN, IBS, CEU). I used the ftp site: >ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz, bu ...
1000genome phase3 eur population whole genome written 15 months ago by Opal0 • updated 15 months ago by Kevin Blighe51k
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Remove duplicated-by-position SNPs using PLINK failed on 1000 Genome phase 3 data
... Hello, I intended to download chr22 genotype data of the 1000Genome phase 3 data (from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/) and extract SNPs in high LD with my selected SNP list (test.txt) using PLINK. Let's say my test.txt file contains only the following line: >rs37614 ...
plink 1000 genome phase 3 duplicated snp id written 15 months ago by Opal0 • updated 15 months ago by Kevin Blighe51k

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