A pedigree is a structured description of the familial relationships between samples.
Some GATK tools (including HaplotypeCaller, GenotypeGVCFs, CalculateGenotypePosteriors and VariantAnnotator) are capable of incorporating pedigree information in the analysis they perform if provided in the form of a PED file through the
-ped) argument. In the case of HC, GGVCFs and VA, the pedigree information is used for calculating annotations that involve population structure (such as Inbreeding Coefficient), but to be clear the pedigree information is not used during the variant calling process itself. This is documented individually in the Tool Doc of each tool. We do not currently maintain an exhaustive list of tools that take pedigree information.
Note that some of the tools that take pedigree information do so optionally, which means that if you forget to provide the pedigree file, the tool will run successfully but pedigree-related annotations will not be produced.
The PED files used as input for GATK tools are based on PLINK pedigree files. The general description can be found here.
For these tools, the PED files must contain only the first 6 (mandatory) columns from the PLINK format PED file, and no alleles, like a FAM file in PLINK:
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.
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.
-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