config_template.txt

### This is a template of the configuration file for CAVA v1.2.3 ###

# Input file format
# Possible values: VCF or TXT | Optional: yes | Default value: VCF
@inputformat = VCF

# Output file format
# Possible values: VCF or TSV | Optional: yes | Default value: VCF
@outputformat =  VCF

# Absolute path to reference genome file
# Possible values: string | Optional: no
@reference = data/tmp.hg38.fa

# Absolute path to Ensembl transcript database file
# Possible values: string | Optional: yes (if not specified, default transcript database will be used)
@ensembl = 

# Absolute path to dbSNP database file
# Possible values: string | Optional: yes
@dbsnp = .

# Are variants with neither transcript nor dbSNP annotation to be included in the output?
# Possible values: TRUE or FALSE | Optional: yes | Default value: TRUE
@nonannot = TRUE

# Are only records with PASS filter value included in the output?
# Possible values: TRUE or FALSE | Optional: yes | Default value: FALSE
@filter = FALSE

# Types of variants to be annotated and outputted
# Possible values: ALL, SUBSTITUTION, INDEL, INSERTION, DELETION or COMPLEX | Optional: yes | Default value: ALL
@type = ALL

# Name of compressed BED file specifying genomic regions variant annotation is restricted to
# Possible values: string | Optional: yes
@target = .

# Name of file providing a list of the gene identifiers variant annotation is restricted to
# Note: gene identifiers need to be given on separate lines in the file
# Possible values: string | Optional: yes
@genelist = .

# Name of file providing a list of transcript identifiers variant annotation is restricted to
# Note: transcript identifiers need to be given on separate lines in the file
# Possible values: string | Optional: yes
@transcriptlist = .

# Name of file providing a list of the dbSNP identifiers variant annotation is restricted to
# Note: dbSNP identifiers need to be given on separate lines in the file
# Possible values: string | Optional: yes
@snplist = .

# Is a log file to be written?
# Possible values: TRUE or FALSE | Optional: yes | Default value: FALSE
@logfile = TRUE

# Which ontology is used for reporting consequence type?
# Possible values: CLASS, SO or BOTH | Optional: yes | Default value: BOTH
@ontology = BOTH

# Definition of variant impact levels (reported by the IMPACT annotation flag)
# Different impact levels are separated by | and a comma-separated list of CLASS terms must be given for each level
# Possible values: string | Optional: yes
# Default value: SG,ESS,FS | SS5,IM,SL,EE,IF,NSY | SY,SS,INT,5PU,3PU
# new IF is initiatior gain (Start gain .. if in phase and in 5'UTR)
@impactdef = SG,ESS,FS | SS5,IM,SL,EE,IF,NSY,IG | SY,SS,INT,5PU,3PU

# Are alternative annotations outputted?
# If TRUE, the ALTANN and ALTCLASS/ALTSO annotation flags are reported instead of the ALTFLAG flag
# Possible values: TRUE or FALSE | Optional: yes | Default value: TRUE
@givealt = TRUE

# Always provide the ALTFLAG output
# If TRUE, the ALTFLAG will always be reported, regardless of the @givalt setting
# Possible values: TRUE or FALSE | Optional: yes | Default value: FALSE
@givealtflag = FALSE

# Number of bases into the intron used as the splice site region
# Possible values: integer >= 6 | Optional: yes | Default value: 8
@ssrange = 8

# Is the prefix CAVA_ added to annotation flag names in VCF output?
# Possible values: TRUE or FALSE | Optional: yes | Default value: FALSE
@prefix = TRUE

# Name of chromosomes you want to run on
# Default = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
@chrom = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT

# Which Codon table should be used?
# 1 = {'ATA': 'I'}   This is the default
# 3 = {'ATA': 'Ile'} This uses the 3 letter code instead
# 4 = {'AGA':'X'} Mitochondrial Code: changes RAGAX, RAGGX, IAUAM, XUGAW (used if chr == M or MT)
# 5 = {'ATA': 'I'} Bacterial code
# Default = 1
@codon_usage = 1
@selenogenes = DIO1,DIO2,DIO3,GPX1,GPX2,GPX3,GPX4,GPX6,SELENOF,SELENOH,SELENOI,SELENOK,SELENOM,SELENON,SELENOO,SELENOP,SELENOS,SELENOT,SELENOU,SELENOV,SELENOW,MSRB1,SEPHS2,TXNRD1,TXNRD2,TXNRD3