Desciption
PedAgree detects autosomal marker incompatibilities. PedAgree needs only pedigree file and doesn't need locus file. The pedigree file have a very strict format because PedAgree need to distinguish markers from other variables. The pedigree file must have the following linkage format :
pedigree ident father mother sex variable1 variable2 ...
Each field must be separated by a tab. Variables can be markers, qualitative or quantitative traits. Marker information must be considered as a field and each allele must be separed by at least a blank. The maximum number of variables in pedigree file is 100, and the maximum size of a record is 1060 characters.
- Pedigree, ident, father and mother can be a string (maximum number of characters is 15).
- sex must be 1 (male) or 2 (female).
- Markers alleles must be numbered alleles (integers between 0 and 160).
Alleles don't need to be recoded. But sometimes, the number of alleles can have a influence on the execution rapidity. If a marker have fewer 160 alleles and if maximum allele number is 160, you must recode alleles.
Inbreeding loops are treated.
Command: PedAgree < file > [ n ] [ > outputfile ]
- file: pedigree file
- [ n ] : optional. n is the maximum number of parental genotypes. Default is 256. n must be larger than 32.
- [ > outputfile ] : optional. to have results on a file and not on screen.
PedAgree uses assembler. A marker with two alleles 4 and 7 is encoding like this:
Algoritm uses logical functions
