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Toy dataset
In GenOtoScope repository all files that will be created for three different variants (each on a different VCF file)
For example for DIAPH1 deletion the input output order is:
-
Annotation of VCF file:
diaph1_deletion.VCF ->
genotoscope_annotate.py
-> diaph1_deletion_annot.VCF and diaph1_deletion_annot.GSvar -
ACMG classification of file:
diaph1_deletion_annot.GSvar ->
genotoscope_classify.py
-> diaph1_deletion_annot_genotoscope.GSvar
** If your VCF contains more variants than one, please consider to use the parameter min_pathogenicity
, as explained here.
Then, if there are variants classified as 4-5 ACMG class or classified as VUS (3 class) with higher pathogenicity probability, than the one you have set, you will see another output file with suffix:
sample_name_pathogenic_vars_genotoscope.GSvar
The *_genotoscope.GSvar
files will contain the classification results based on GenOtoScope, organized in the following columns:
ACMG_rules: list of examined ACMG evidence-based criteria and the triggering output of each
ACMG_rules_comment: explanation of triggering (or not) each examined ACMG evidence-based criteria
ACMG_rule_flags: warning flags collected through the automatic examination
ACMG_class_preferred: ACMG class (Benign, Likely Benign, VUS, Likely Pathogenic, Pathogenic) for preferred inheritance mode
ACMG_class_numeric_preferred: ACMG class (1, 2, 3, 4, 5) for preferred inheritance mode
ACMG_class_prob_preferred: Pathogenicity probability for preferred inheritance mode
ACMG_class_alternative: same as ACMG_class_preferred but for the alternative inheritance mode, if applicable
ACMG_class_numeric_alternative: same as ACMG_class_numeric_alternative but for alternative inheritance mode, if applicable
ACMG_class_prob_alternative: same as ACMG_class_prob_preferred but for alternative inheritance mode