Following the pedigree id is the individual/subject id. This is an alphanumeric identifier for this individual and is unique within the individual’s family.
Next is the id of the father. This identifier corresponds to the father's individual ID or "0" if the father is unknown. Note: if a father ID is specified, the father must also appear in the file.
Next is the id of the mother. This identifier corresponds to the mother's individual ID or "0" if unknown mother. Note: if a mother ID is specified, the mother must also appear in the file.
Following the mother’s id is the individual's sex and affection status (0=UNKNOWN, 1=UNAFFECTED, 2=AFFECTED).
After this information for each marker, both marker alleles are listed. Each marker is represented by two columns, one for each allele, separated by a space and coded either ACGT or 1-4 where: 1=A, 2=C, 3=G, T=4. The number '0' in any of the marker genotype positions indicates missing data. The order of the markers must correspond to the order of the marker names in the first row of the file. Missing values here must be encoded with a `0', unlike the phenotype file.
You can open a few example files inside the HelixTree application folder with WordPad or Notepad (xbat.ped, qtl.ped or CAMP.ped).
For more information see the section Importing Family-Based Data section of the HelixTree Manual.
http://www.goldenhelix.com/SNP_Variation/Manual/importing_data.html
