Parameters

The help message may be viewed by running:

gnali --help

Mandatory

gNALI requires the path to the input file. The remaining parameters will revert to default settings. The following is the minimum number of command line parameters required to run gNALI:

gnali
    --input /path/to/input/file

The following parameters are required by gNALI:

Option Alternative Parameter Description
-i --input txt or tsv or csv A list of input genes (as HGNC symbols), separated by newlines. Genes in non-standard formats will not be analyzed, and their regions will be logged in the output directory. An example of a valid input file can be found here.

Optional

The optional parameters can be used to add additional functionality. Some will be assigned default values if unspecified.

Databases

The following parameter relates to the database queried:

Option Alternative Parameter Description
-d --database string Database to query for variants. Defaults to gnomADv2.1.1 if unspecified.

gNALI can use:

The following parameters relate to custom configuration files:

Option Alternative Parameter Description
-c --config yaml Path to a configuration file (see below). Defaults to gNALI's own configuration file (with support for gnomADv2.1.1 and gnomADv3.1.1) if unspecified.
None --config_template_grch37 None Running gNALI with this parameter will generate a fillable configuration file template in the current directory for a VCF database using the GRCh37 reference genome.
None --config_template_grch38 None Running gNALI with this parameter will generate a fillable configuration file template in the current directory for a VCF database using the GRCh38 reference genome.

Filtering

The following command-line parameters relate to variant filtering:

Option Alternative Parameter Description
-p --predefined_filters string Filter variants with predefined filters. Using the help command will show available filters for each supported database. To use several filters, separate them with a space.
-a --additional_filters string Filter variants based on the INFO column in the VCF database. Enclose in quotes. To use several filters, separate them with a space. An example can be found here. More info as well as filters available for natively supported databases can be found here.

Output

The following command-line flags relate to gNALI output:

Option Alternative Parameter Description
-o --output /path/to/output/directory Path to an output directory (must not exist yet). Defaults to results-<id> if unspecified.
-f --force None Overwrite an existing directory.

The following command-line flags relate to gNALI additional output:

Option Alternative Parameter Description
-P --pop_freqs None If selected, gNALI will find the allele count (AC), allele number (AN), and allele frequency (AF) by population group for every variant passing filtering. This information will be included in the detailed output file. An example can be found here.
None --vcf None If selected, gNALI will generate an additional output file, a VCF file containing headers from the database selected and all variants passing filtering. An example can be found here.
-v --verbose None Turns on verbose error logging.