Joint Genotyper Options
You can run the Joint Genotyper from a multisample VCF, a multisample gVCF, or directly from a set of single sample gVCFs.
The following parameters are available for Joint Genotyper.
| • | --enable-joint-genotyping |
To run the Joint Genotyper, set to true.
| • | --output-directory |
The output directory. --output-directory is required.
| • | --output-file-prefix |
The prefix used to label all output files. --output-file-prefix is required.
| • | -r |
The directory where the hash table resides.
| • | --variant or --variant-list |
Specifies the path to a single gVCF file. You can specify multiple gVCF files using multiple --variant options. A maximum of 200 gVCFs are supported. Use --variant-list to specify a file containing a list of gVCF files that need to be combined using one variant file path per line.
| • | --pedigree-file |
Specify the path to a pedigree file describing the relationship between samples. For more information, see Pedigree Mode.