Proband file


The proband file has the format as the pedigree structure file. A proband file should be used with the pedigree structure file. The individual specified in the proband file should be also in the pedigree structure file. If you are simulating disease status, SeqSIMLA will simulate the same affection status as the affection status for the individuals specified in the proband file.

For example,

FAM1 3 1 2 1 1
FAM1 5 3 4 1 2
FAM2 6 1 2 1 2

Then the three individuals in the simulated files will have the same affection status as specified.

If you are simulating a threshold quantitative trait, 1 in the 6th column means the trait value for the person is below the lower bond of the threshold and 2 means the trait value for the person is above the upper bond of the threshold. For example, if lower and upper bonds are specified as 50 and 100, respectively, individual 3 in FAM1 will have trait value < 50 and individuals 5 in FAM1 and individual 3 in FAM2 will have trait values > 100. See the options -extreme and -extreme2 for more details of simulating a threshold trait. You can set people with missing genotype by adding 0 in column 7.

For example,

FAM1 3 1 2 1 1
FAM1 5 3 4 1 2 0
FAM2 6 1 2 1 2

Related options: -proband, -famfile, -extreme, -extreme2