Toy dataset

Example input and output for variants

Order of input and output files

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:

1. Annotation of VCF file:

   diaph1_deletion.VCF -> genotoscope_annotate.py -> diaph1_deletion_annot.VCF and diaph1_deletion_annot.GSvar

2. 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

GenOtoScope output columns

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