ancestrymap format descriptionancestrymap format. The ancestrymap format
can be used as an input format for genotypic matrices in the functions
pca, lfmm and snmf.
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
ancestrymap2lfmm
ancestrymap2geno
geno
lfmm.data
ped
vcf