gVCF Genotyper Options

The gVCF Genotyper uses a set of single sample gVCFs to output a multisample VCF that contains one entry per variant seen in any of the input gVCFs. Genotypes cannot be adjusted using population information.

The gVCF Genotyper does not require a hash table. It is recommended to disable it using the command --enable-map-align=false.

The following parameters are available for gVCF Genotyper.

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--enable-gvcf-genotyper

To enable the gVCF Genotyper, set to true.

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--ht-reference

The file containing the reference sequence in FASTA format. --ht-reference is required.

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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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--gg-output-format

The output file format. The default value is vcf.gz. The permitted output file formats are vcf.gz, vcf, or bcf. Only the vcf.gz format is compatible with the joint genotyper. If using a different format, you can convert the format using the open-source bcftools utility.

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--gg-regions

The file specifying the regions to run the gVCF Genotyper in. Variants outside these regions are ignored. The file can either be a bed file or a list of genomic regions specified using chromosome:start-end. Genomic regions can be separated by commas or line breaks. If using exome or enrichment data, specify the list of regions targeted by the probes to limit additional time spent processing unreliable genotype variants that lie outside the targeted regions.

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--gg-enable-concat

Concat output for genomic regions into a single output file. By default, the value is set to true.

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--gg-max-alternate-alleles

Maximum number of alternate alleles. By default, the value is set to 50.

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--gg-enable-indexing

Build a tabix index for the output file. By default, the value is set to false. The --gg-output-format must be set to vcf.gz to use --gg-enable-indexing.

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--gg-drop-genotypes

Select to output only the alleles for each variant. By default, the value is set to false. --gg-drop-genotypes is equivalent to running bcftools view -G on the default output.

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--gg-allele-list

[Optional] Force the output of genotypes at specified sites. The path of a vcf.gz or bcf file containing the sites must be included.