ancestrymap: 'ancestrymap' format description
In LEA: LEA: an R package for Landscape and Ecological Association Studies

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Description of the ancestrymap format. The ancestrymap format can be used as an input format for genotypic matrices in the functions pca, lfmm and snmf.

The ancestrymap format has one row for each genotype. Each row has 3 columns: the 1st column is the SNP name, the 2nd column is the sample ID, the 3rd column is th number of alleles. Genotypes for a given SNP name are written in consecutive lines. The number of alleles can be the number of reference alleles or the number of derived alleles. Missing genotypes are encoded by the value 9.

Here is an example of a genotypic matrix using the ancestrymap format with 3 individuals and 4 SNPs:

rs0000    SAMPLE0    1
rs0000    SAMPLE1    1
rs0000    SAMPLE2    2
rs1111    SAMPLE0    0
rs1111    SAMPLE1    1
rs1111    SAMPLE2    0
rs2222    SAMPLE0    0
rs2222    SAMPLE1    9
rs2222    SAMPLE2    1
rs3333    SAMPLE0    1
rs3333    SAMPLE1    2
rs3333    SAMPLE2    1