Comparison of allele frequencies between population
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5 months ago
elisheva ▴ 110

Hi all,
I would like to examine whether the frequencies of many alleles differ between the African and North European populations.
I downloaded the 1000 genome project wgs vcf file via the FTP site: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
But the allele frequencies are given for super populations, thus the European population includes Spain and Italy.
Does anyone familiar with this kind of data and could help?

Thanks

SNP vcf 1000 genome project population • 301 views
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5 months ago
  1. Download the pedigree file from https://www.internationalgenome.org/faq/can-i-get-phenotype-gender-and-family-relationship-information-samples/ .
  2. Define your European subpopulation, and create a file with just the sample IDs within that subpopulation with e.g. a short shell script.
  3. Compute allele frequencies using just those samples. This can be done efficiently with e.g. plink2 --vcf <VCF file> --keep <sample ID file> --freq.
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Thanks for your response.
It seems that the versions of the vcf file and the pedigree file are different.
I couldn't find the matching version for both files.
Is there is any option to solve this?

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The pedigree file contains some samples that were excluded from the phase 3 VCF, but that's okay, the extra sample IDs will just be ignored by --keep.

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Apparently, there are no sample Ids in the vcf file I posted, and I couldn't find any others.

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Oh, that's because you downloaded the sites VCF instead of the full genotypes VCF. Download a .genotypes.vcf.gz file from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ instead, or the plink2-formatted version from https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 .

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