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
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
norpredict
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 theoffline
option to use the local database for annotation (you must have previously downloaded it using thehmtnote dump
command). Ifcsv
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 providedoutput_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