3.1 Introduction to pedcheck

pedcheck reads the pedigree file and checks for errors in the pedigree structure. Specifically, it checks for the following errors:

• duplicate names of individuals
• individuals (non--founders) with parents missing from the pedigree
• individuals with parents of the wrong gender
• impossible pedigrees, such as an individual who is her or his own ancestor
• invalid names, genders, integers or real numbers
• pedigree entries with missing data

If no errors are found, pedcheck reports the number of components (connected pedigrees) found and lists for each component:

• number of individuals
• the number of founders
• the number of females
• the number of males
• the number of unsexed individuals
• the number of observed individuals
• the name of the first member of the component, in chronological order

If there are changes to the file, pedcheck writes an output pedigree file. Requested changes may include reordering of the pedigree chronologically (by component, then by name), the addition of gender, the addition of an observed indicator, and reversing the order of the parental names.

Other MORGAN programs do their own pedigree checking by calling the relevant pedcheck functions, but it is still useful to do preliminary processing of data files first.