Combine gVCF Options

You can run Combine gVCFs on a set of single sample gVCFs and multisample gVCFs to create a single multisample gVCF as output. For large-scale population calling, use gVCF Genotyper instead of the Combine gVCF Genotyper.

The following parameters are available for combine gVCFs:

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--enable-combinegvcfs

To run Combine gVCFS, set to true.

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--intermediate-results-dir

[Optional] Set the intermediate results to a directory different from the output directory, such as /staging/temp. If running Combine gVCFs, --intermediate-results-dir is recommended. For more information, see Determine Input and Output File Locations.

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--output-directory

The output directory. --output-directory is required.

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--output-file-prefix

The prefix used to label all output files. --output-file-prefix is required.

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-r

The directory where the hash table resides.

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--variant or --variant-list

Specifies the path to a single gVCF file. You can specify multiple gVCF files using multiple --variant options. 200 gVCFs are supported, but it is not recommended to combine more than 10 gVCFS. 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.