text: user2867: I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems.
  To do that, I've read a lot of papers and books in order to understand the main concepts and how the algorithms to this task work.
  However, is been very hard for me to understand the organization of the huge amount of genomic data available over the internet.. HapMap, 1000 Genomes, dbSNP and so on... (!) I downloaded GB of data from different sources, but I really do not know what to do with then.
  --
  To be more specific in my question:
  First I would like to run a Genetic Algorithm to find the tag SNP based on a simple linkage disequilibrium coverage measure. The authors of this GA used the following data
  
  Three published SNP data sets were downloaded from HapMap (http://www.hapmap.org/) (NOT AVAILABLE ANYMORE) for evaluating the prediction accuracies achievable by our method:
  • ENr112. 343 SNPs genotyped in population ASW (African ancestry in Southwest USA) on chromosome 2 from position 51512208 to 52012208. The genotypes of 83 individuals were used.
  • ENr113. 380 SNPs genotyped in population ASW on chromosome 4 from position 118466103 to 118966103. The genotypes of 83 individuals were used.
  • ENm013. 683 SNPs genotyped in population ASW on chromosome 7 from position 89621624 to 90736048. The genotypes of 83 individuals were used.
  
  Besides that, the authors stated that
  
  We represent a genotype g_i of length L by a sequence over {0, 1, 2}^L (since we assume only bi-allelic SNPs). 0 and 1 stand for the minor and major homozygous types respectively, meaning that the two alleles at that SNP locus are either 0 or 1; the major and minor alleles are determined by the frequency at which each allele appears in the population. A value of 2 denotes the heterozygous type for an SNP having two different alleles.
  
  And also
  
  To obtain phasing of genotypes, we used the GEVALT algorithm.
  
  I believe they obtain the aforementioned data in genotype format (something with 0, 1 and 2 values only) and then phasing it to apply in the problem. The image below is a example of this process.
  
  So
  
  How and where can I download these data?
  I know HapMap is not available due to a security issue but there are the FTP, but the FTP folders are really complex to understand. Can someone guide me to download data from there?
  
  I hope I made myself clear.
  
  user73: The HapMap website was suspended due to a security issue. Archived HapMap data is available via FTP, but it's a better idea to download up-to-date International Genome data from the IGSR website (which includes the HapMap individuals as a subset).
  The format you use will be dependent on the data analysis program you're using. In most cases involving SNP analysis, the VCF format is probably what would be used.
  
original_text: 2867: <p>I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems.</p>
  <p>To do that, I've read a lot of papers and books in order to understand the main concepts and how the algorithms to this task work.</p>
  <p>However, is been very hard for me to understand the organization of the huge amount of genomic data available over the internet.. HapMap, 1000 Genomes, dbSNP and so on... (!) I downloaded GB of data from different sources, but I really do not know what to do with then.</p>
  <p>--</p>
  <p>To be more specific in my question:</p>
  <p>First I would like to run a <a href="https://link.springer.com/content/pdf/10.1007%2Fs12539-012-0060-x.pdf" rel="nofollow noreferrer">Genetic Algorithm</a> to find the tag SNP based on a simple linkage disequilibrium coverage measure. The authors of this GA used the following data</p>
  <blockquote>
  <p>Three published SNP data sets were downloaded from HapMap (<a href="http://www.hapmap.org/" rel="nofollow noreferrer">http://www.hapmap.org/</a>) <em><strong>(NOT AVAILABLE ANYMORE)</strong></em> for evaluating the prediction accuracies achievable by our method:</p>
  <p>• ENr112. 343 SNPs genotyped in population ASW (African ancestry in Southwest USA) on chromosome 2 from position 51512208 to 52012208. The genotypes of 83 individuals were used.</p>
  <p>• ENr113. 380 SNPs genotyped in population ASW on chromosome 4 from position 118466103 to 118966103. The genotypes of 83 individuals were used.</p>
  <p>• ENm013. 683 SNPs genotyped in population ASW on chromosome 7 from position 89621624 to 90736048. The genotypes of 83 individuals were used.</p>
  </blockquote>
  <p>Besides that, the authors stated that</p>
  <blockquote>
  <p>We represent a genotype g_i of length L by a sequence over {0, 1, 2}^L (since we assume only bi-allelic SNPs). 0 and 1 stand for the minor and major homozygous types respectively, meaning that the two alleles at that SNP locus are either 0 or 1; the major and minor alleles are determined by the frequency at which each allele appears in the population. A value of 2 denotes the heterozygous type for an SNP having two different alleles.</p>
  </blockquote>
  <p>And also</p>
  <blockquote>
  <p>To obtain phasing of genotypes, we used the GEVALT algorithm.</p>
  </blockquote>
  <p>I believe they obtain the aforementioned data in genotype format (something with 0, 1 and 2 values only) and then phasing it to apply in the problem. The image below is a example of this process.</p>
  <p><img src="https://image.ibb.co/dptixo/imagem.png" alt="from paper" /></p>
  <p>So</p>
  <ol>
  <li>How and where can I download these data?</li>
  <li>I know HapMap is not available due to a security issue but there are the FTP, but the FTP folders are really complex to understand. Can someone guide me to download data from there?</li>
  </ol>
  <p>I hope I made myself clear.</p>
   73: <p>The HapMap website was suspended due to <a href="https://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/" rel="nofollow noreferrer">a security issue</a>. Archived HapMap data is available <a href="ftp://ftp.ncbi.nlm.nih.gov/hapmap/" rel="nofollow noreferrer">via FTP</a>, but it's a better idea to download up-to-date International Genome data from the <a href="http://www.internationalgenome.org/data" rel="nofollow noreferrer">IGSR website</a> (which includes the HapMap individuals as a subset).</p>
  
  <p>The format you use will be dependent on the data analysis program you're using. In most cases involving SNP analysis, the VCF format is probably what would be used.</p>
  