Command Line Parameters

Illumina Connected Annotation supports the following command line parameters:

Option(s)	Description
--cache, -c	Input cache directory
--in, -i	Input VCF path
--tsv	Input TSV path
--out, -o	Output file prefix (.json.gz will be added to complete the file path)
--ref, -r	Input compressed reference sequence path
--sd	Input supplementary annotation directory
--sources, -s	Annotation data sources to be used (comma-separated list of supported tags)
--credentials-file, -l	File path to user credentials (default: ~/.ilmnAnnotations/credentials.json)
--versions-config	Annotation version config file (default: ~/.ilmnAnnotation/<assembly>_annotation_config.json)
--ignore-license-error	Ignore error due to invalid license and skip related data sources
--force-mt	Forces annotation of mitochondrial variants
--legacy-vids	Enables support for legacy VIDs
--enable-dq	Report DQ from VCF samples field
--enable-bidirectional-fusions	Enables support for bidirectional gene fusions
--disable-junction-preservation	Disable junction preserving functional annotation
--str	User-provided STR annotation TSV file
--vcf-info	Additional VCF info field keys (comma-separated) desired in the output
--vcf-sample-info	Additional VCF format field keys (comma-separated) desired in the output
--sa-cutoff	SVs ≥ this value will not have supplementary annotations
--simple-nomenclature-cutoff-length	SVs ≥ this value will have simple nomenclature annotation (default: 1000)
--output-format	Output file format (options: json, vcf)
--help, -h	Displays the help menu
--version, -v	Displays the version

Most of the options are self explanatory. In the following sections, we provide more details about some that may not be obvious:

--force-mt

For hg19 genome assembly, the default behavior is to skip annotating the mitochondrial chromosome. This can be overridden using this flag.

--disable-junction-preservation

By default, junction preserving behavior as described in Junction Preserving Annotation is enabled. This flag can turn it off.

--vcf-info

Illumina Connected Annotations does not pass all VCF info fields to the output JSON. If the user is interested in any particular field, they may request them to be passed using this parameter. Multiple info field keys need to be comma separated.

--vcf-sample-info

Illumina Connected Annotations does not pass all sample fields to the output JSON. If the user is interested in any particular field, they may request them to be passed using this parameter. Multiple format field keys need to be comma separated.