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

#---------------
# Family Barcode
#---------------
#Grouping sample names together help grouping the naming of the files with the same prefix (fam1_ for all family members) and to define automatically a specific barcode, the "familyBarcode".
#As an example, 2 families where the fam1 corresponds to a trio sequencing (proband and parents) and fam2 with 2 affected child.

#fam1: Sample1 Sample2 Sample3 
#fam2: Sample4 Sample5

#-----------------
# VaRank Options :
#-----------------

#-vcfInfo:		no
#-metrics:              us
#-nowebsearch:          yes
#-rsfromvcf:            no
#-Homstatus:            no
#-Homcutoff:            80
#-SSFcutoff:            -5
#-NNScutoff:            -10
#-MEScutoff:            -15
#-phastConsCutoff:      0.95
#-readFilter:           10
#-readPercentFilter:    15
#-depthFilter:          10
#-freqFilter:           0.01
#-rsFilter:             removeNonPathoRS
#-S_Known:		110
#-S_Fs:			100
#-S_Nonsense:		100
#-S_EssentialSplice:	90
#-S_StartLoss:		80
#-S_StopLoss:		80
#-S_CloseSplice:	70
#-S_Missense:		50
#-S_DeepSplice:		25
#-S_Inframe:		40
#-S_Synonymous:		10


