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Trinary genetic data format

The Trinary data format (extension should be “.tri” or “.trinary”) is a simple format derived form the Serono GMX format to manage case-control association studies using bi-allelic markers (mainly SNPs).


<nbIndividuals> <nbMarkers>
<pheno1> <pheno2> …
<markerID1> <chromosome> <localisation> <geno1.1> <geno1.2> …
<markerID2> <chromosome> <localisation> <geno2.1> <geno2.2> …

The fields have to be separated by simple space. The first, thrid and fifth lines must be inchanged. First comes the dimension of the data with the number of total individuals introduced in the study and the number of markers considered. Then the phenotype of each individuals, 1 for cases and 0 for controls. Finally for each marker we have to specify the ID of the marker, on which chromosome it stands and its localisation (in bp or cm). For each individual, it follows the genotype attached to the marker. 0 and 2 code for the two homozygote types, 1 for the heterozygote type and 3 code for missing-values.


6 3
1 1 1 1 0 0
SNP_A 12 85489 0 2 0 3 1 2
SNP_B 12 85495 2 2 0 0 1 3
SNP_C 12 85499 1 3 0 2 1 2

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logiciels/lhisa/trinary_gen_data.txt · Last modified: 2014/11/28 15:51 (external edit)

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