I was given a maize SNP dataset in the HapMap format and I was curious how I can infer the genotype given this particular format (see picture below). I understand that for HapMAp data the second column contains the allele information (i.e. all possible alleles at this locus) and that columns 12 and onward contain the appropriate allele for the sequenced individual. However, I'm unsure of how to derive the genotype of a diploid when only one allele is given. I realise there is a function in R for reading raw HapMap data (see http://svitsrv25.epfl.ch/R-doc/library/snpMatrix/html/read.HapMap.data.html) but I'm not even sure it's still operational. Any information would be a help. Much thanks!
Hi James,
I did not work with hapmap data for long, but I remember that some genotype files were available.
I think (but not sure) that column named 0 and 1 refer to the same individual. you could check that by counting columns and the number of individuals.
Hope it help.
Hi James,
Previously I have used www.hapmap.org but this website doesn't work now.
I suggest you to go to
1000 genomw website.
https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/
56
Hi James,
Some websites on attachment 1
https://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/
7
https://svitsrv25.epfl.ch/R-doc/library/snpMatrix/html/read.HapMap.data.html
9
https://www.nature.com/nature/journal/v426/n6968/full/nature02168.html
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https://bioinfo.cs.technion.ac.il/projects/Anvar-Tzur/website/genotype_data.html
15
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-484
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https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-484
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https://egp.gs.washington.edu/workshop/download/Day1_1045am_Nickerson.pdf
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https://catalog.coriell.org/1/NIGMS/Collections/More/Samples-with-Sequencing-Data
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