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Description
When running a new version v3.4.5 there is no WARNING message, that GeneHancer data is not set (like it was before, while running AnnotSV for the first time after installation)
Now, when run AnnotSV v3.4.5 I can see message:
...listing of the annotations to be realized (July 22 2025 - 17:36)
...CytoBand annotation
...Genes annotation
...RefSeq annotation
...Regulatory elements annotations
...Promoter annotations
...EnhancerAtlas annotations
...GeneHancer annotations
So apperently AnnotSV uses GeneHancer?
I don't see any GeneHancer files here:
AnnotSV/share/AnnotSV/Annotations_Human/FtIncludedInSV/RegulatoryElements/GRCh38$ ls
ABC_ENSEMBL_GRCh38.sorted.bed EA_RefSeq_GRCh38.sorted.bed MPRA_ENSEMBL_GRCh38.sorted.bed miRTargetLink_RefSeq_GRCh38.sorted.bed promoter_3500bp_ENSEMBL_GRCh38.sorted.bed
ABC_RefSeq_GRCh38.sorted.bed GH_ENSEMBL_GRCh38.sorted.bed MPRA_RefSeq_GRCh38.sorted.bed promoter_1500bp_ENSEMBL_GRCh38.sorted.bed promoter_500bp_ENSEMBL_GRCh38.sorted.bed
EA_ENSEMBL_GRCh38.sorted.bed GH_RefSeq_GRCh38.sorted.bed miRTargetLink_ENSEMBL_GRCh38.sorted.bed promoter_2500bp_ENSEMBL_GRCh38.sorted.bed promoter_500bp_RefSeq_GRCh38.sorted.bed
Also this instruction seems to have no effct:

Is the GeneHancer indeed used?
Best regards
DamianL
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