Command line interface

All options

Each options here has an one-to-one mapping to an attribute of CharGerConfig by replacing all the dashes with underscores. For example, --input maps to CharGerConfig.input, and --pathogenic-variant maps to CharGerConfig.pathogenic_variant.

usage: charger [-h] [--version] --input VCF [--output TSV] [--pathogenic-variant VCF] [--hotspot3d-cluster TSV] [--override-variant-info] [--include-vcf-details]
               [--inheritance-gene-table TSV] [--disease-specific] [--PP2-gene-list TXT] [--BP1-gene-list TXT]
               [--override-acmg-score 'MODULE=SCORE MODULE=SCORE ...'] [--override-charger-score 'MODULE=SCORE MODULE=SCORE ...'] [--clinvar-table TABIX]
               [--rare-threshold FREQ] [--common-threshold FREQ] [--min-pathogenic-score INT] [--min-likely-pathogenic-score INT] [--max-likely-benign-score INT]
               [--max-benign-score INT]

Named Arguments

--version

show program’s version number and exit

--input

Path to the input VCF to be annotated

--output

Path to CharGer output

--pathogenic-variant

Path to the known pathogenic variants

--hotspot3d-cluster

Path to HotSpot3D clusters result

--override-variant-info

Override the variant info using ClinVar description

Default: False

--include-vcf-details

Include the VCF details in the output

Default: False

ACMG modules

--inheritance-gene-table

Path to inheritance gene tab separated table and enable PVS1 module. Table columns must be: gene, disease, mode_of_inheritance.

--disease-specific

Enable disease specific inheritance-gene-table detection

Default: False

--PP2-gene-list

Path to PP2 gene list (list of gene symbols)

--BP1-gene-list

Path to BP1 gene list (list of gene symbols)

--override-acmg-score

Override the default scoring of ACMG modules

It overrides the default score for each ACMG module defined by _default_acmg_scores and stores the final scores at CharGerConfig.acmg_module_scores.

CharGer modules

--override-charger-score

Override the default scoring of CharGer modules

It overrides the default score for each CharGer module defined by _default_charger_scores and stores the final scores at CharGerConfig.charger_module_scores.

Annotation sources

--clinvar-table

Path to the Tabix indexed ClinVar table

Thresholds

--rare-threshold

Maximal allele frequency to be a rare variant

Default: 0.0005

--common-threshold

Minimal allele frequency to be a common variant

Default: 0.005

Score thresholds

--min-pathogenic-score

Minimal total score for a variant to be pathogenic

Default: 9

--min-likely-pathogenic-score

Minimal total score for a variant to be likely pathogenic

Default: 5

--max-likely-benign-score

Maximal total score for a variant to be likely benign

Default: -4

--max-benign-score

Maximal total score for a variant to be benign

Default: -8