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9 Command file: Genetic analysis 1519.4 Reading in the pedigree fileThe syntax for specifying a pedigree file in the ASReml command file ispedigree file[qualifiers]• the qualifiers 1 are listed in Table 9.1,• the identities (individual, male parent, female parent) are merged into a singlelist and the inverse relationship is formed before the data file is read,• when the data file is read, data fields with the !P qualifier are recoded accordingto the combined identity list,• the inverse relationship matrix is automatically associated with factors codedfrom the pedigree file unless some other covariance structure is specified. Theinverse relationship matrix is specified with the variance model name AINV,• the inverse relationship matrix is written to ainverse.bin,– if ainverse.bin already exists ASReml assumes it was formed in a previousrun and has the correct inverse– ainverse.bin is read, rather than the inverse being reformed (unless !MAKEis specified); this saves time when performing repeated analyses based on aparticular pedigree,– delete ainverse.bin or specify !MAKE if the pedigree is changed betweenruns,• identities are printed in the .sln file,– identities should be whole numbers less than 200,000,000 unless !ALPHA isspecified,– pedigree lines for parents must precede their progeny,– unknown parents should be given the identity number 0,– if an individual appearing as a parent does not appear in the first column, itis assumed to have unknown parents, that is, parents with unknown parentagedo not need their own line in the file,– identities may appear as both male and female parents, for example, inforestry.1 A white paper downloadable from http://www.vsni.co.uk/resources/doc/ contains detailsof these options.