2.4 Pedigree file

The pedigree file may contain two sections, formatting statements and pedigree data, separated by the file separator `****'. The first section is optional; if present, it contains statements that describe the contents and format of the pedigree file, as some MORGAN users find it convenient to describe the pedigree data within the file itself. The alternative is to put these formatting statements in the parameter file.

The pedigree data begin below the file separator. Data for each individual must be placed on a separate line. Each line begins with three names, followed by integers, then real numbers. The only required fields, the three "names", are identifiers for each individual and his or her parents. Names may include up to 15 alphanumeric characters. Whitespace (comma, space, tabs, linefeed), single (') and double (") quotes, and the hash mark (#) cannot be included in names. Names longer than 15 characters are truncated to 15 characters. Pedigree founders should be given parents with names `0'.

Gender, if present, is the fourth item in each line. These three or four values may be followed by an "observed" indicator, with values of `0', indicating an unobserved individual, or `1', indicating an observed individual. The optional "observed" indicator is followed by other integers, if present, and real numbers, if present. Integers and real numbers can represent individuals' trait data.

The format of the file is flexible and is specified by the user with `input pedigree record ...' statements, described in the next section.

Unlike LINKAGE format pedigree files, genotype data are not included in a MORGAN pedigree file.