Pedigree Mode

Use pedigree mode to jointly analyze samples from related individuals and to perform de novo calling.

To invoke pedigree mode set the --enable-joint-genotyping option to true and use the --pedigree-file option to specify the path to a pedigree file that describes the relationship between panels.

The pedigree file must be a tab-delimited text file with the file name ending in the .ped extension. The following information is required.

Column Header	Description
Family_ID	The pedigree identifier.
Individual_ID	The ID of the individual.
Paternal_ID	The ID of the individual's father. If the founder, the value is 0.
Maternal_ID	The ID of the individual's mother. If the founder, the value is 0.
Sex	The sex of the sample. If male, the value is 1. If female, the value is 2.
Phenotype	The genetic data of the sample. If unknown, the value is 0. If unaffected, the value is 1. If affected, the value is 2.

The following is an example of an input pedigree file.

#Family_ID Individual_ID   Paternal_ID    Maternal_ID    Sex Phenotype
FAM001     NA12877_Father  0              0              1   1
FAM001     NA12878_Mother  0              0              2   1
FAM001     NA12882_Proband NA12877_Father NA12878_Mother 2   2
FAM001     NA12883_Proband NA12877_Father NA12878_Mother 1   0

To compare multiple pedigrees, you can run gVCF Genotyper on the output of Joint Genotyper and merge multiple joint-called pedigrees into a single multisample VCF.

Use the --vc-emit-ref-confidence gVCF option to configure the Joint Genotyper to write a multisample GVCF.