API

Command Line Interface

hmtnote annotate

Annotate a VCF file using data from HmtVar.

If neither --basic, --crossref, --variab nor --predict are provided, they will all default to True, and the VCF will be annotated using all the available information. If no internet connection is available, use the --offline option to use the local database for annotation (you must have previously downloaded it using the hmtnote dump command). If csv is set to True, an additional annotated CSV file will be produced (along with the annotated VCF file) with the same base name and in the same path as the provided output_vcf argument.

hmtnote annotate [OPTIONS] INPUT_VCF OUTPUT_VCF

Options

-b, --basic

Annotate VCF using basic information (locus, pathogenicity, etc.) (default: False)

-c, --crossref

Annotate VCF using cross-reference information (Clinvar and dbSNP IDs, etc.) (default: False)

-v, --variab

Annotate VCF using variability information (nucleotide and aminoacid variability, allele frequencies) (default: False)

-p, --predict

Annotate VCF using predictions information (from MutPred, Panther, Polyphen and other resources) (default: False)

-o, --offline

Annotate VCF using previously downloaded databases (offline mode) (default: False)

-C, --csv

Produce an additional annotated CSV file (default: False)

Arguments

INPUT_VCF

Required argument

OUTPUT_VCF

Required argument

hmtnote dump

Download databases from HmtVar for offline annotation.

hmtnote dump [OPTIONS]

Python Module

hmtnote.hmtnote.annotate(input_vcf: str, output_vcf: str, basic: bool = False, crossref: bool = False, variab: bool = False, predict: bool = False, offline: bool = False, csv: bool = False)[source]

Annotate a VCF file using information from HmtVar.

If neither basic, crossref, variab nor predict are provided, they will all default to True, and the VCF will be annotated using all the available information. If no internet connection is available, use the offline option to use the local database for annotation (you must have previously downloaded it using the hmtnote dump command). If csv is set to True, an additional annotated CSV file will be produced (along with the annotated VCF file) with the same base name and in the same path as the provided output_vcf argument.

Parameters

  • input_vcf (str) – input VCF file to annotate

  • output_vcf (str) – file where the annotated VCF will be saved

  • basic (bool) – annotate VCF using basic information (locus, pathogenicity, etc.) (default: False)

  • crossref (bool) – annotate VCF using cross-reference information (Clinvar and dbSNP IDs, etc.) (default: False)

  • variab (bool) – annotate VCF using variability information (nucleotide and aminoacid variability, allele frequencies) (default: False)

  • predict (bool) – annotate VCF using predictions information (from MutPred, Panther, Polyphen and other resources) (default: False)

  • offline (bool) – annotate VCF using previously downloaded databases (offline mode) (default: False)

  • csv (bool) – produce an additional annotated CSV file

(default: False)

Returns

hmtnote.hmtnote.dump()[source]

Download databases from HmtVar for offline annotation.

Returns