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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.

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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.

from paper

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.

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  • $\begingroup$ I have update the entire question in order to make it clearer. $\endgroup$
    – William Tenorio
    Jun 5, 2018 at 13:37
  • $\begingroup$ 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. $\endgroup$
    – llrs
    Jun 5, 2018 at 14:25
  • $\begingroup$ 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). $\endgroup$
    – William Tenorio
    Jun 5, 2018 at 14:29
  • $\begingroup$ 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. $\endgroup$
    – William Tenorio
    Jun 5, 2018 at 14:37
  • $\begingroup$ 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 $\endgroup$
    – llrs
    Jun 5, 2018 at 14:41

1 Answer 1

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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.

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  • $\begingroup$ 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. $\endgroup$
    – William Tenorio
    May 30, 2018 at 20:02

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