A pedigree is a structured description of the familial relationships between samples.
Some GATK tools are capable of incorporating pedigree information in the analysis they perform if provided in the form of a PED file through the
PED files are tabular text files describing meta-data about the samples. See http://www.broadinstitute.org/mpg/tagger/faq.html and http://zzz.bwh.harvard.edu/plink/data.shtml#ped for more information.
The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:
The IDs are alphanumeric: the combination of family and individual ID should uniquely identify a person. If an individual's sex is unknown, then any character other than 1 or 2 can be used in the fifth column.
A PED file must have 1 and only 1 phenotype in the sixth column. The phenotype can be either a quantitative trait or an "affected status" column: GATK will automatically detect which type (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed).
Affected status should be coded as follows:
If any value outside of -9,0,1,2 is detected, then the samples are assumed to have phenotype values, interpreted as string phenotype values.
Note that genotypes (column 7 onwards) cannot be specified to the GATK.
You can add a comment to a PED or MAP file by starting the line with a # character. The rest of that line will be ignored, so make sure none of the IDs start with this character.
Each -ped argument can be tagged with NO_FAMILY_ID, NO_PARENTS, NO_SEX, NO_PHENOTYPE to tell the GATK PED parser that the corresponding fields are missing from the ped file.
Here are two individuals (one row = one person):
FAM001 1 0 0 1 2 FAM001 2 0 0 1 2