The structure file for fastSTRUCTURE seem to be a table with rows and columns but the cells are all numbers, while my genotypes are simply bases. How could I know what I should insert there?

  • $\begingroup$ What format are your genotypes in at the moment? There is likely some tool someone has written to convert it to the correct format. $\endgroup$ – user438383 Sep 23 '20 at 12:22
  • $\begingroup$ Just table of 'A/C' bases $\endgroup$ – hiddenhospitalresearch Sep 23 '20 at 12:40
  • $\begingroup$ 'Table' isn't a format. What are the rows? What are the columns? Is it genotypes or alleles - i.e. is there one or two rows per marker? the more info you give, the easier it will be for someone to help you. Could you add a sample of your genotype format to the main answer so others can see it. $\endgroup$ – user438383 Sep 23 '20 at 12:41

Numbers, usually in the form of 0/1/2, is a common way many formats represent bases.

For example, if a SNPs has bases which are A/T, then these are encoded as 0/1, with the reference allele/base taking the 0 and the alternate allele/base taking 1.

However, if you read the documentation, it says:

Specifically, rows in the data file correspond to samples, with two rows per sample (note that only diploids are handled by this software), and columns correspond to SNPs. The first 6 columns of the file will be ignored; these typically would include IDs, metadata, etc. This software only handles bi-allelic loci. The two alleles at each locus can be encoded as desired; however, missing data should be encoded as `-9'.

So you should be able to use your base letters here and it will work OK as long as the columns and rows are formatted correctly.


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