config.ini

[InterVar]
buildver = hg19 
# hg19 
inputfile = example/ex1.avinput
# the inputfile and the path  example/ex1.avinput hg19_clinvar_20151201.avinput
# tab-delimited will be better for including the other information
inputfile_type = AVinput
# the input file type VCF(vcf file with single sample),AVinput,VCF_m(vcf file with multiple samples)
outfile = example/myanno
# the output file location and prefix of output file
database_intervar = intervardb
# the database location/dir for Intervar
lof_genes = %(database_intervar)s/PVS1.LOF.genes
pm1_domain = %(database_intervar)s/PM1_domains_with_benigns
mim2gene = %(database_intervar)s/mim2gene.txt
# morbidmap = %(database_intervar)s/morbidmap.txt
# disabled for BP5 as reviewer suggested. for OMIM, only mim2gene.txt needed. 
mim_recessive = %(database_intervar)s/mim_recessive.txt
mim_domin = %(database_intervar)s/mim_domin.txt
mim_adultonset = %(database_intervar)s/mim_adultonset.txt
mim_pheno = %(database_intervar)s/mim_pheno.txt
mim_orpha = %(database_intervar)s/mim_orpha.txt
#orpha = %(database_intervar)s/orpha.txt
orpha = %(database_intervar)s/orpha.txt.utf8
knowngenecanonical = %(database_intervar)s/knownGeneCanonical.txt
pp2_genes = %(database_intervar)s/PP2.genes
bp1_genes = %(database_intervar)s/BP1.genes
ps1_aa = %(database_intervar)s/PS1.AA.change.patho
# do not add the builder version
ps4_snps = %(database_intervar)s/PS4.variants
# do not add the builder version
bs2_snps = %(database_intervar)s/BS2_hom_het
# do not add the builder version
exclude_snps = %(database_intervar)s/ext.variants
# do not add the builder version,the variant in this list will not check the frequency, it is causal.
# the list should be tab-delimited,format like this:
# Chr Pos Ref_allele Alt_allele
evidence_file = None
# add your own Evidence file for each Variant:
# evidence file as tab-delimited,format like this:
# Chr Pos Ref_allele Alt_allele  PM1=1;BS2=1;PP2=0
disorder_cutoff = 0.01
#It is for BS1: Allele frequency is greater than expected for disorder
[InterVar_Bool]
onetranscript = FALSE 
# TRUE or FALSE: print out only one transcript for exonic variants (default: FALSE/all transcripts)
otherinfo = TRUE               
# TRUE or FALSE: print out otherinfo (infomration in fifth column in queryfile,default: FALSE)
# this option only perform well with AVinput file,and the other information only can be put in the fifth column.  The information in >5th column will be lost.
# When input as  VCF or VCF_m files with otherinfo option, only het/hom will be kept, depth and qual will be lost.
[Annovar]
# the ANNOVAR version should be >=  2016-02-01, older verions of ANNOVAR will bring problems.
convert2annovar = ./convert2annovar.pl
#convert input file to annovar format
table_annovar = ./table_annovar.pl
# table_annovar.pl of file location
annotate_variation = ./annotate_variation.pl
# annotate_variation of file location
database_locat = humandb 
# the database location/dir from annnovar   check if database file exists
#database_names = refGene esp6500siv2_all 1000g2015aug avsnp147 dbnsfp33a clinvar_20190305 gnomad_genome dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene
database_names = refGene esp6500siv2_all 1000g2015aug avsnp147 dbnsfp42a clinvar_20210501 gnomad_genome dbscsnv11 rmsk ensGene knownGene
# specify the database_names from ANNOVAR or UCSC
[Other]
current_version = Intervar_20210727 
# pipeline version
public_dev = https://github.com/WGLab/InterVar/releases