requires a file describing the genealogical data and a selection flag
indicating which individuals will be considered in the clustering process
and/or in the optional sub-pedigree reconstruction. A separate list of
individuals could be also provided in separate files to overriding the
pedigree file describes the relationships between individuals using a
standard format. Each row of the file describes a single individual and
has the following standard format:
GenealogyID PersonID FatherID MotherID Sex
GenealogyID is a numeric code,
unique within the genealogy.
PersonID is a numeric code
that uniquely identifies an individual.
and MotherID are the numeric
codes that specify the individual’s parents. If an individual is a
founder each parent identifier field contains a “0”, otherwise the two
parents should be present in the same family.
Sex field contains “1” for a male or “2” for a female.
SelectionFlag field contains
“2” if the individual must be included in the clustering process analysis
or “0” if the individual must not be included in the cluster. If the aim
of the study is generating sub-pedigrees suitable for family-based
studies we would like to include in the sub-pedigrees all the
first-degree related individuals having genotype data. This information
is provided setting the SelectionFlag
fields must be separated by a single TAB or by comma.
parents and two sons. The sons will be included in the clustering
process, the mother has genotypic data.
1 1 0 0 1 0
1 2 0 0 2 1
1 3 1 2 1 2
1 4 1 2 1 2
default extension for a genealogy file is “ped”.
the lists of individuals to be included in the clustering process or in
the sub-pedigree reconstruction step could be provided in separated files
listing one PersonID on each
line. These data will overwrite the information given in the genealogical
file and allows using a single genealogical file for different studies.
Attention PersonID,FatherID and MotherID have to be numeric and not larger than 32000. Thanks to Clemens Egger we can provide an en/decoding tool.