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For a a few SNPs from given gene, I know there happen to be several haplotypes that most of the population has. But from a person's data on those SNPs, we have two alleles at each SNP, so it's not trivial to match the SNP data to infer the person's haplotypes. When I search this I find tools that seem to be for haplotype reconstruction and SNP imputation, such as SHAPEIT, but this is not what I'm looking for.

Might someone know of a tool for this inference of known haplotypes from SNP data? It would be helpful even if someone could give me a name for this problem, as I'm not sure of the right term to search.

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It depends on the scale of the data (i.e. number of individuals, number of SNPs). Generally this can be done by matching up individual SNP genotypes to haplotype tag SNPs. The specific combination of genotyped SNPs is used to determine the underlying haplotype, based on tag SNP frequencies for each haplotype.

More details of the process of identifying tag SNPs can be found here:

https://www.broadinstitute.org/haploview/tagger

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  • $\begingroup$ The scale is quite small: only 4 SNPs and ~1k people. Tagger seems to want a local copy of HapMap data to identify tag SNPs, so it's probably overkill. I think it'll be best for me to look at how tagger works and implement my own function. $\endgroup$ – user1799035 Jan 22 at 1:47

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