# This file is used to simplify the configuration of AnnotSV.
# Anything behind a hashtag is considered as a comment
# Please, feel free to change the AnnotSV options.

#------------------
# AnnotSV Options :
#------------------

-annotationMode:            "both"

-benignAF:                  0.01

-candidateGenesFiltering:   0

-genomeBuild:               GRCh38

-hpo:                       ""

-includeCI:                 1

-metrics:                   "us"

-minTotalNumber:            "500"

-overlap:                   100

-overwrite:                 1

-promoterSize:              500

-rankFiltering:             "1-5,NA"

-reciprocal:                0

-snvindelPASS:              0

-SVinputInfo:               1

-SVminSize:                 50

-vcf:			    0


#------------------------
# AnnotSV Output columns:
#------------------------
# Output column names are listed below.
# In order to disable default annotations provided by AnnotSV, some column names (the ones that are not marked with an *) can be commented with a hash character ("#") by the user.

AnnotSV_ID                      *
SV_chrom                        *
SV_start                        *
SV_end                          *
SV_length                       *
SV_type                         *
Samples_ID                      *
Annotation_mode                 *

# Genes annotations:
Gene_name                       *
Gene_count                      *
Tx                              *
Tx_start                        *
Tx_end                          *
Exon_count
Overlapped_tx_length            *
Overlapped_CDS_length           *
Frameshift                      *
Location                        *
Location2                       *
Dist_nearest_SS                 *
Nearest_SS_type                 *
Intersect_start                 *
Intersect_end                   *

# Regulatory Elements annotations:
RE_gene                         *

# Annotations with benign genes or genomic regions:
B_gain_source                   *
B_gain_coord                    *
B_gain_AFmax                    *
B_loss_source                   *
B_loss_coord                    *
B_loss_AFmax                    *
B_ins_source                    
B_ins_coord                     
B_ins_AFmax                     
B_inv_source                    
B_inv_coord
B_inv_AFmax
po_B_gain_allG_source                   
po_B_gain_allG_coord                    
po_B_gain_someG_source
po_B_gain_someG_coord
po_B_loss_allG_source
po_B_loss_allG_coord
po_B_loss_someG_source
po_B_loss_someG_coord
po_B_loss_source                   
po_B_loss_coord                    

# Annotations with pathogenic genes or genomic regions:
P_gain_phen 
P_gain_hpo 
P_gain_source 
P_gain_coord 
P_loss_phen 
P_loss_hpo 
P_loss_source 
P_loss_coord
P_ins_phen
P_ins_hpo
P_ins_source
P_ins_coord
P_inv_phen
P_inv_hpo
P_inv_source
P_inv_coord
po_P_gain_phen
po_P_gain_hpo
po_P_gain_source
po_P_gain_coord
po_P_gain_percent
po_P_loss_phen
po_P_loss_hpo
po_P_loss_source
po_P_loss_coord
po_P_loss_percent

# Annotations with pathogenic snv/indel:
P_snvindel_nb
P_snvindel_phen

# Cancer
Cosmic_ID
Cosmic_mut_typ

# Breakpoints annotations
TAD_coordinate
ENCODE_experiment
GC_content_left
GC_content_right
Repeat_coord_left
Repeat_type_left
Repeat_coord_right
Repeat_type_right
Gap_left
Gap_right
SegDup_left
SegDup_right
ENCODE_blacklist_left
ENCODE_blacklist_characteristics_left
ENCODE_blacklist_right
ENCODE_blacklist_characteristics_right

# Gene-based annotations:
ACMG
HI                              *
TS                              *
GenCC_disease   
GenCC_moi       
GenCC_classification    
GenCC_pmid
DDD_status
DDD_mode
DDD_consequence
DDD_disease
DDD_pmid
DDD_HI_percent
ExAC_synZ
ExAC_misZ
ExAC_delZ
ExAC_dupZ
ExAC_cnvZ
LOEUF_bin
ExAC_pLI                        
GnomAD_pLI                      *
OMIM_morbid                     *
OMIM_morbid_candidate           *
OMIM_ID
OMIM_phenotype
OMIM_inheritance
Exomiser_gene_pheno_score
Human_pheno_evidence
Mouse_pheno_evidence
Fish_pheno_evidence

# Ranking:
AnnotSV_ranking_score           *
AnnotSV_ranking_criteria        *
ACMG_class                      *

