configfile

# 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 :
#------------------


# puts below the path of the bedtools executable
-bedtools:		""
-genomeBuild:           GRCh37

-overlap:               70

-promoterSize:		500

-SVinputInfo:           1

-SVminSize:		50

-vcfPASS:               0

-annotationfolder       ""


#----------------------------------------------------------------
# SV type configuration is requiered to access to the SV ranking:
#----------------------------------------------------------------
## class 1 = benign
## class 2 = likely benign
## class 3 = VOUS (variant of unknown significance)
## class 4 = likely pathogenic
## class 5 = pathogenic
#
# To classify SV into 1 of 5 classes according to the ACMG guidelines, 
# AnnotSV needs to retrieve the SV type (duplication, deletion, ...) in the input SV file (BED or VCF)

## From a VCF SV input file:
############################
# To access to the SV ranking from a VCF input file, the INFO keys used for structural variants should follow the VCF Version 4.2 Specification:
# - The "SVTYPE" values should be one of DEL, INS, DUP, INV, CNV, BND
# - The <CN0>, <CN2>, <CN3>... angle-bracketed ID from the "ALT" column should be used in case of SVTYPE=CNV in the INFO column
#  
## From a BED SV input file:
############################
# To access to the SV ranking from a BED input file, the column number with the SV type information should be indicated:
-svtBEDcol:	-1 
# (for example, if the SV type column is the 4th column, then user should set -svtBEDcol to 4)
# The "SVTYPE" values should be one of the following:
# Deletion: DEL, deletion or <CN0>
# Insertion: INS or insertion
# Duplication: DUP, duplication, <CN2>, <CN3>...
# Inversion: INV or inversion
# Breakend record: BND, breakpoint, breakend