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.