# This file can be given as a input to VariantFilter tool
# Lines that start with "#" are comments lines and will be ignored

### IMPORTANT ###
# any argument given in this file will overwrite
# any corresponding argument given in command line
# Don't change this argument
filterfile True

# path to input table
tableinput input.csv

# path to output table
tableoutput output.csv

# desired chromosomes can be given in any order separated by spaces
# but can't be given in any number maximum is 24.
chromosome 1 2 21 X Y

# desired chromosomal positions intervals separated by spaces
position 1:300-500 12:500-600 22:12000-150000

# zygosity 1/1 for homozygote 0/1 for heterozygote
# this works in an opposite way i.e.
# if 1/1 is given this will return anything other than 0/1
zygosity 1/1

# returns read depth values over given threshold i.e.
# any read depth over 20 in this case
readdepth 20

# Any number of genes with HGNC symbols can be given separated by spaces
genelist BRC1A SCN1A HOX PAX8

# filters both "gnomad_maf" and "minor_allele_frequency" columns
# returns variant with maf values lesser than given threshold
maf 0.01

# variant consequences
consterms missense_variant stop_gained frame_shift

# biotype
biotype protein_coding pseudo_gene

# search given term in "phenotypes" column.
# multiple search terms can be given separated by spaces
omim mental retardation epilepsy

# these arguments can be given with "only_" prefix
# without prefix this will return given term and empty rows
# with prefix it will return only the rows that contain the term
# multiple terms can be given separated by spaces
polyphen probably_damaging

# same as polyphen
sift deleterious

# same as sift
clinsig pathogenic

# this argument will drop transcripts if position of the change,
# gene name, and variant consequence are the same
drop True
