VARPIN - Variant Prioritization and Interpretation for Genetic Analysis

Create Setting File


Database Selection

Please select the database you wish to use.

filter

filter_score

info

cancer_somatic

population

prediction


Display Only Selection

The selected database will display information in the final report only, and it will not include in the calculation process.

filter

filter_score

info

cancer_somatic

population

prediction


Variable

(* meaning that system will use a default value if the blank value has been detected. )

Group Variable

filter_score
mode *
Filtering mode of this group
(Default: 1 + Remove varaint if Benign and not be a splicing site in regsnpintron. )

Database Variable

filter

func_refgene
filter_list *
(Default: exonic splicing ncRNA_exonic ncRNA_intronic ncRNA_splicing intronic )
mode *
0: filtered if in filter_list | 1: filtered if not in filter_list
(Default: Keep variant if matched with filter_list )
exonic_refgene
filter_list *
(Default: synonymous SNV unknown )
mode *
0: filtered if in filter_list | 1: filtered if not in filter_list
(Default: REMOVE variant if matched with filter_list )
aachange
gene_name_list
Gene name that you wish to find (1 line per gene name)
(Default: (No value) )
refseq_list
Refseq accession number that you wish to find (1 line per number)
(Default: (No value) )
exon_list
Exon name that you wish to find (1 line per exon name)
(Default: (No value) )
coding_ref_list
Coding DNA reference sequence that you wish to find (1 line per refseq)
(Default: (No value) )
protein_ref_list
Protein reference sequence that you wish to find (1 line per refseq)
(Default: (No value) )

filter_score

exonic_refgene_score
list *
Determine which exonic function prefered to be seen first in the report.
(Default: frameshift insertion frameshift deletion frameshift substitution stopgain stoploss )
regsnpintron_disease
disease_mode *
Mode of scoring
(Default: 0/0.5/1 (Benign/Possibly Damaging/Damaging) )
dbsc_snv_ada
threshold_ada *
Specified threshold to distinguish data between benign and deleterious (ADA Score Only) (Min: 0 / Max: 1)
(Default: 0.6 )
dbsc_snv_rf
threshold_rf *
Specified threshold to distinguish data between benign and deleterious (RF Score Only) (Min: 0 / Max: 1)
(Default: 0.6 )

population

1000g
threshold *
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
(Default: 0.05 )
exac
threshold *
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
(Default: 0.05 )
esp6500
threshold *
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
(Default: 0.05 )
gnomad_exome
threshold *
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
(Default: 0.05 )
gnomad_genome
threshold *
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
(Default: 0.05 )

prediction

revel
weight *
Weight of this database
(Default: 1.9262 )
sift
weight *
Weight of this database
(Default: 0.9924 )
polyphen2_hdiv
weight *
Weight of this database
(Default: 0.9228 )
polyphen2_hvar
weight *
Weight of this database
(Default: 1.0794 )
mutation_taster
weight *
Weight of this database
(Default: 1.664 )
mutation_assessor
weight *
Weight of this database
(Default: 1.1849 )
vest3
weight *
Weight of this database
(Default: 1.4583 )
lrt
weight *
Weight of this database
(Default: 0.958 )
metasvm
weight *
Weight of this database
(Default: 1.0051 )
metalr
weight *
Weight of this database
(Default: 1.0468 )
cadd
weight *
Weight of this database
(Default: 1.0301 )
dann
weight *
Weight of this database
(Default: 0.964 )
fathmm_mkl
weight *
Weight of this database
(Default: 0.921 )
gerp
weight *
Weight of this database
(Default: 0.997 )
fathmm
weight *
Weight of this database
(Default: 1.3344 )
provean
weight *
Weight of this database
(Default: 1.1105 )
phastcons20way
weight *
Weight of this database
(Default: 0.9393 )
phastcons100way
weight *
Weight of this database
(Default: 1.0137 )
siphy
weight *
Weight of this database
(Default: 0.9098 )