annotsv capturing genes fusion event

[cdbope]

Hi all,

I was wondering if the genes fusion event can be extracted from annotSV output file. For example in the column "AnnotSV_ranking_criteria", you can have genes listed like : 1A (cf Gene_count, RE_gene, +0.00);2A (cf P_gain_source, +1.00);2H-2 (AFF3/CNGA3/EDAR/LIPT1/POU3F3/SLC5A7, +0.00);2L (VWA3B, +0.00);3C (157 genes, +0.90);5F (+0.00).

Those genes listed can be forming a fusion events?

[lgmgeo]

AnnotSV is not specifically dedicates to genes fusion.

cf #203

For example in the column "AnnotSV_ranking_criteria"

See https://lbgi.fr/AnnotSV/Documentation/Scoring_Criteria_AnnotSV_latest.xlsx to understand the AnnotSV_ranking_criteria.

, you can have genes listed like : 1A (cf Gene_count, RE_gene, +0.00);2A (cf P_gain_source, +1.00);2H-2 (AFF3/CNGA3/EDAR/LIPT1/POU3F3/SLC5A7, +0.00);2L (VWA3B, +0.00);3C (157 genes, +0.90);5F (+0.00).
Those genes listed can be forming a fusion events?

=> Your SV example overlaps 157 genes, this is a large SV.

2H-2 (AFF3/CNGA3/EDAR/LIPT1/POU3F3/SLC5A7,

Overlap with HI gene / morbid gene fully contained within observed copy-number gain…
2H-2. …and patient phenotype is either inconsistent with what has been described for this HI gene / morbid gene (Exomiser_gene_pheno_score < 0.7) OR unknown.