Genotyper Options
This section provides information on the options available for each of the genotypers.
gVCF Options
In addition to the standard parameters for the variant caller stage of the DRAGEN host software, the following parameters are available to create a gVCF:
| • | --vc-emit-ref-confidence |
To enable banded gVCF generation, set to GVCF. To enable base pair resolution gVCF generation, set to BP_RESOLUTION. Banded gVCF generation is enabled by default and recommended. BP_Resolution results in large files that slow down any subsequent analysis.
| • | --vc-gvcf-gq-bands |
The --vc-gvcf-gq-bands option defines genotype quality (GQ) bands values. If the GQ values for positions homozygous to the reference lie within the same band, the positions homozygous to the reference are grouped into the same block.
| • | --vc-max-alternate-alleles |
The --vc-max-alternate-alleles option specifies the maximum number of ALT alleles that are output in VCF or gVCF. The default value is 6.
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.
gVCF Genotyper can also read gVCF files from an S3 bucket. For gVCF files in a public bucket, URLs with the prefix s3:// or https:// can be used in --variant or --variant-list. If the bucket requires authentication, environment variables or config files can be used. See the Samtools website for information on the htslib AWS S3 plugin.
gVCF Genotyper needs access to the index file for each gVCF input. The URLs for each gVCF and index file needs to be combined as https://url1.gvcf.gz##idx##https://url2.gvcf.gz.tbi, and then passed to --variant or --variant-list on the command line.
The following parameters are available for gVCF Genotyper.
| • | --enable-gvcf-genotyper |
To enable the gVCF Genotyper, set to true.
| • | --ht-reference |
The file containing the reference sequence in FASTA format. --ht-reference is required.
| • | --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.
| • | --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.
| • | --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.
| • | --gg-enable-concat |
Concat output for genomic regions into a single output file. By default, the value is set to true.
| • | --gg-max-alternate-alleles |
Maximum number of alternate alleles. By default, the value is set to 50. If there are more alleles than the set limit, alleles are ranked by frequency of occurrence in the input samples. The most common k alleles are output.
| • | --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.
| • | --gg-extra-params=--min-depth=X |
[Optional]Remove false-positive variant calls. Values for genotypes (FORMAT/GT) in samples with read depth (FORMAT/DP) below the threshold are set to missing. The default threshold is 8.
| • | --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.
| • | --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.
| • | --gg-extra-params=--remove-nonref |
[Optional]Removes the <NON_REF> symbolic allele from the output of gVCF Genotyper. This option should be used to support downstream tools which cannot process VCF lines with <NON_REF>.
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.
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:
| • | --enable-combinegvcfs |
To run Combine gVCFS, set to true.
| • | --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.
| • | --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. 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.