Body: <p>I am trying to reproduce the results from this paper <a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-6-r88" rel="nofollow noreferrer">&quot;Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences&quot;</a>.</p>
  <p>Specifically I want to extract  high differentiated  ( or less) SNPs from 1k Genome data set representing high proportion of the population present.</p>
  <p>The paper mentioned using Vcffixup from Vcflib (<a href="https://github.com/vcflib/vcflib" rel="nofollow noreferrer">https://github.com/vcflib/vcflib</a>) but there might still be other things I am missing.</p>
  <ul>
  <li>Update 2 (MWE)</li>
  </ul>
  <p>So this is my code snippet.</p>
  <pre><code>## to dowload datafile, from linux terminal, use curl or wget
  curl -O https://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
  ### unzip the file
  gunzip dowloaded file
  ### take the first few lines from the vcf file.
  ### since actual file is huge, the name of sfile for testing is 
  ### myfile.vcf
  head -200 downloadedfile &gt; myfile.vcf 
  </code></pre>
  <p>Now the next section was done in python environment (jupyter notebook).</p>
  <pre><code>## using the library pysam
  from pysam import VariantFile
  import pandas as pd 
  with VariantFile(test_datafile) as vcf_reader:
  for record in vcf_reader:
      sample_file = record.samples.keys() 
      alleles = [record.samples[x].allele_indices for x in record.samples]
      break ## just to make sure my data is as intended
  </code></pre>
  <p>Now to the VCF tools part - vcffixup was used in the paper.</p>
  <pre><code>## Install vcflib
     sudo apt-get install libvcflib-tools libvcflib-dev
  ### export path
     export PATH=$PATH:/usr/lib/vcflib/bin 
  ### refresh enviroment variables
     source ~/.bashrc 
  ## run vcffixup
    vcffixup myfile.vcf
  </code></pre>
  <p>A sample of vcffixup output is hown below:
  <a href="https://i.sstatic.net/R7SlY.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/R7SlY.png" alt="enter image description here" /></a></p>
  <p>So the questions questions I have is:</p>
  <ol>
  <li>how to compute derived allele frequency differences at all variants for pairs of continent and pairs of population within continent</li>
  </ol>
  <p>Thanks!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-24T21:27:48.323Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-25T23:06:33.490Z
Comments.Text: Thanks for the edit! But how do we choose the snps? And what do you mean by present? Present in which sample of the multi sample vcf file? And do you care about zygosity? I mean, the vcf is already what you want:it has 0/0 when a variant is absent.
Comments.UserDisplayName: terdon
Tags: <vcf><snp><1000genomes>
Title: SNPs with high population differentiation from 1k Genome dataset
ThreadText: # SNPs with high population differentiation from 1k Genome dataset
  
  (Asked by: username_0 on 2022-08-24)
  
  I am trying to reproduce the results from this paper ["Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences"](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-6-r88).
  
  Specifically I want to extract high differentiated ( or less) SNPs from 1k Genome data set representing high proportion of the population present.
  
  The paper mentioned using Vcffixup from Vcflib (<https://github.com/vcflib/vcflib>) but there might still be other things I am missing.
  
  * Update 2 (MWE)
  
  So this is my code snippet.
  
  ```
  ## to dowload datafile, from linux terminal, use curl or wget
  curl -O https://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
  ### unzip the file
  gunzip dowloaded file
  ### take the first few lines from the vcf file.
  ### since actual file is huge, the name of sfile for testing is 
  ### myfile.vcf
  head -200 downloadedfile > myfile.vcf 
  
  ```
  
  Now the next section was done in python environment (jupyter notebook).
  
  ```
  ## using the library pysam
  from pysam import VariantFile
  import pandas as pd 
  with VariantFile(test_datafile) as vcf_reader:
  for record in vcf_reader:
      sample_file = record.samples.keys() 
      alleles = [record.samples[x].allele_indices for x in record.samples]
      break ## just to make sure my data is as intended
  
  ```
  
  Now to the VCF tools part - vcffixup was used in the paper.
  
  ```
  ## Install vcflib
     sudo apt-get install libvcflib-tools libvcflib-dev
  ### export path
     export PATH=$PATH:/usr/lib/vcflib/bin 
  ### refresh enviroment variables
     source ~/.bashrc 
  ## run vcffixup
    vcffixup myfile.vcf
  
  ```
  
  A sample of vcffixup output is hown below:
  [![enter image description here](https://i.sstatic.net/R7SlY.png)](https://i.sstatic.net/R7SlY.png)
  
  So the questions questions I have is:
  
  1. how to compute derived allele frequency differences at all variants for pairs of continent and pairs of population within continent
  
  Thanks!
  
  **Tags:** vcf, snp, 1000genomes
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Thanks for the edit! But how do we choose the snps? And what do you mean by present? Present in which sample of the multi sample vcf file? And do you care about zygosity? I mean, the vcf is already what you want:it has 0/0 when a variant is absent.  
  
  ---
  
  ## 0 answers
  
  