Answers.Body: <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>
  
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Answers.CreationDate: 2018-05-30T20:02:55.900Z
Answers.Text: Ok, gringer. Thanks for your reply. But it seems I need to be more specific in my answer. To do that, I copy a definition used a paper I was reading.
  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. A value of 2 denotes the heterozygous type for an SNP having two different alleles.
  Which type of data do you think was used in that problem?
  What I know for now is that the authors considered firstly the genotyped data and after phased the corresponding haplotypes.
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Answers.CreationDate: 2018-05-28T23:28:52.343Z
Answers.LastActivityDate: 2018-05-28T23:28:52.343Z
Answers.UserDisplayName: gringer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T13:37:31.427Z
Comments.Text: I have update the entire question in order to make it clearer.
Comments.UserDisplayName: William Tenorio
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T14:25:32.843Z
Comments.Text: Could you clarify to which FTP folders do you refer? Could you provide a link? Also the question is about obtaining the data or about the genetic algorithm used? It seems to like two questions mixed together.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T14:29:51.590Z
Comments.Text: Llopis the question is about obtaining SNP data. I provide details about the paper I'm trying to reproduce in order to make easier to someone help me to find the data which could be used in this specific algorithm. About the FTP folder, I unfortunately have not enough knowledge to be more specific (I actually do not know which folder I need to download).
Comments.UserDisplayName: William Tenorio
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T14:37:04.913Z
Comments.Text: Maybe this helps (I could after update the question):  I study the VCF format as suggested by another user here, and I think it can be useful for me. However, I do not know how to filter the data to the specific population, chromosome and position considered in the question.
Comments.UserDisplayName: William Tenorio
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T14:41:58.090Z
Comments.Text: Sorry but no, it doesn't help. That this data can be used for an algorithm is not relevant to find it or download it. If you don't know a FTP site, then it is better not to mention any site at all. I'll propose some changes, review them and accept them if you think I improved your main question
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T14:43:00.687Z
Comments.Text: Wait, you already downloaded GB of data? Are this from the HapMap project as you wished or not?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T14:52:04.463Z
Comments.Text: I downloaded data from this link https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html which is used in IMPUTE2 program (I've read in some paper that the genotype data was phased using this program) but it not seems to help. 
  
  I also downloaded the VCF content from 1000 Genomes FTP using ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/  but as I said I do not know how to filter the information.
Comments.UserDisplayName: William Tenorio
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-05T15:16:59.437Z
Comments.Text: To better help you, you need to ask one question each time (to avoid confusions like this one to future readers). One step each time. So, you already have the data you want or not? The goal of this question is to help you obtaining the data you want if you already have it we can't help because you don't need it.   
  If you want to ask for how to filter that information or how to run an analysis you can always ask a new question, with what you have, what is your goal and what you tried.
Comments.UserDisplayName: llrs
Tags: <snp><public-databases><genomics><data-download><haplotypes>
Title: How to download SNP data from specific regions, population and positions?
ThreadText: # How to download SNP data from specific regions, population and positions?
  
  (Asked by: username_0 on 2018-05-28)
  
  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](https://link.springer.com/content/pdf/10.1007%2Fs12539-012-0060-x.pdf) 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.
  
  ![from paper](https://image.ibb.co/dptixo/imagem.png)
  
  So
  
  1. How and where can I download these data?
  2. 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.
  
  **Tags:** snp, public-databases, genomics, data-download, haplotypes
  
  > **Comments:**
  > **username_0**: I have update the entire question in order to make it clearer.  
  > **username_1**: Could you clarify to which FTP folders do you refer? Could you provide a link? Also the question is about obtaining the data or about the genetic algorithm used? It seems to like two questions mixed together.  
  > **username_0**: Llopis the question is about obtaining SNP data. I provide details about the paper I'm trying to reproduce in order to make easier to someone help me to find the data which could be used in this specific algorithm. About the FTP folder, I unfortunately have not enough knowledge to be more specific (I actually do not know which folder I need to download).  
  > **username_0**: Maybe this helps (I could after update the question):  I study the VCF format as suggested by another user here, and I think it can be useful for me. However, I do not know how to filter the data to the specific population, chromosome and position considered in the question.  
  > **username_1**: Sorry but no, it doesn't help. That this data can be used for an algorithm is not relevant to find it or download it. If you don't know a FTP site, then it is better not to mention any site at all. I'll propose some changes, review them and accept them if you think I improved your main question  
  > **username_1**: Wait, you already downloaded GB of data? Are this from the HapMap project as you wished or not?  
  > **username_0**: I downloaded data from this link https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html which is used in IMPUTE2 program (I've read in some paper that the genotype data was phased using this program) but it not seems to help.   I also downloaded the VCF content from 1000 Genomes FTP using ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/  but as I said I do not know how to filter the information.  
  > **username_1**: To better help you, you need to ask one question each time (to avoid confusions like this one to future readers). One step each time. So, you already have the data you want or not? The goal of this question is to help you obtaining the data you want if you already have it we can't help because you don't need it.    If you want to ask for how to filter that information or how to run an analysis you can always ask a new question, with what you have, what is your goal and what you tried.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-05-28. Score: 2
  
  The HapMap website was suspended due to [a security issue](https://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/). Archived HapMap data is available [via FTP](ftp://ftp.ncbi.nlm.nih.gov/hapmap/), but it's a better idea to download up-to-date International Genome data from the [IGSR website](http://www.internationalgenome.org/data) (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.
  
  > **Comments:**
  > **username_0**: Ok, username_2. Thanks for your reply. But it seems I need to be more specific in my answer. To do that, I copy a definition used a paper I was reading. 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. A value of 2 denotes the heterozygous type for an SNP having two different alleles. Which type of data do you think was used in that problem? What I know for now is that the authors considered firstly the genotyped data and after phased the corresponding haplotypes.  
  
  ---
  
  