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Database Selection
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filter
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func_refgene
exonic_refgene
gene_refgene
aachange
zygosity
filter_score
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exonic_refgene_score
regsnpintron_disease
regsnpintron_splicing_site
dbsc_snv_ada
dbsc_snv_rf
info
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intervar
clinvar
cancer_somatic
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cosmic84
nci60
population
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1000g
dbsnp
exac
esp6500
gnomad_exome
gnomad_genome
prediction
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revel
sift
polyphen2_hdiv
polyphen2_hvar
mutation_taster
mutation_assessor
vest3
lrt
metasvm
metalr
cadd
dann
fathmm_mkl
gerp
fathmm
provean
phastcons20way
phastcons100way
siphy
cadd_raw
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Display Only Selection
The selected database will display information in the final report only, and it will not include in the calculation process.
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filter
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func_refgene
exonic_refgene
gene_refgene
aachange
zygosity
filter_score
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exonic_refgene_score
regsnpintron_disease
regsnpintron_splicing_site
dbsc_snv_ada
dbsc_snv_rf
info
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intervar
clinvar
cancer_somatic
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cosmic84
nci60
population
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1000g
dbsnp
exac
esp6500
gnomad_exome
gnomad_genome
prediction
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revel
sift
polyphen2_hdiv
polyphen2_hvar
mutation_taster
mutation_assessor
vest3
lrt
metasvm
metalr
cadd
dann
fathmm_mkl
gerp
fathmm
provean
phastcons20way
phastcons100way
siphy
cadd_raw
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Variable
(
*
meaning that system will use a default value if the blank value has been detected. )
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Group Variable
filter_score
mode
*
Filtering mode of this group
== Not Selected ==
Remove varaint if no data in regsnpintron and dbsc_snv only.
1 + Remove varaint if Benign and not be a splicing site in regsnpintron.
1 + Remove varaint if score lower than threshold in dbsc_snv.
1 + Remove varaint if Benign and not be a splicing site in regsnpintron OR score lower than threshold in dbsc_snv.
1 + Remove varaint if Benign and not be a splicing site in regsnpintron AND score lower than threshold in dbsc_snv.
Use Default Value
(Default: 1 + Remove varaint if Benign and not be a splicing site in regsnpintron. )
Database Variable
filter
func_refgene
filter_list
*
exonic
splicing
ncRNA_exonic
ncRNA_intronic
ncRNA_splicing
UTR5
UTR3
intronic
upstream
downstream
intergenic
Use Default Value
(Default: exonic splicing ncRNA_exonic ncRNA_intronic ncRNA_splicing intronic )
mode
*
0: filtered if in filter_list | 1: filtered if not in filter_list
== Not Selected ==
REMOVE variant if matched with filter_list
Keep variant if matched with filter_list
Use Default Value
(Default: Keep variant if matched with filter_list )
exonic_refgene
filter_list
*
frameshift insertion
frameshift deletion
frameshift substitution
stopgain
stoploss
nonframeshift insertion
nonframeshift deletion
nonframeshift substitution
nonsynonymous SNV
synonymous SNV
unknown
N/A
Use Default Value
(Default: synonymous SNV unknown )
mode
*
0: filtered if in filter_list | 1: filtered if not in filter_list
== Not Selected ==
REMOVE variant if matched with filter_list
Keep variant if matched with filter_list
Use Default Value
(Default: REMOVE variant if matched with filter_list )
aachange
gene_name_list
Gene name that you wish to find (1 line per gene name)
Use Default Value
(Default:
(No value)
)
refseq_list
Refseq accession number that you wish to find (1 line per number)
Use Default Value
(Default:
(No value)
)
exon_list
Exon name that you wish to find (1 line per exon name)
Use Default Value
(Default:
(No value)
)
coding_ref_list
Coding DNA reference sequence that you wish to find (1 line per refseq)
Use Default Value
(Default:
(No value)
)
protein_ref_list
Protein reference sequence that you wish to find (1 line per refseq)
Use Default Value
(Default:
(No value)
)
filter_score
exonic_refgene_score
list
*
Determine which exonic function prefered to be seen first in the report.
frameshift insertion
frameshift deletion
frameshift substitution
stopgain
stoploss
nonframeshift insertion
nonframeshift deletion
nonframeshift substitution
nonsynonymous SNV
synonymous SNV
unknown
N/A
Use Default Value
(Default: frameshift insertion frameshift deletion frameshift substitution stopgain stoploss )
regsnpintron_disease
disease_mode
*
Mode of scoring
== Not Selected ==
0/0.5/1 (Benign/Possibly Damaging/Damaging)
-1/0.5/1 (Benign/Possibly Damaging/Damaging)
Use Default Value
(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)
Use Default Value
(Default: 0.6 )
dbsc_snv_rf
threshold_rf
*
Specified threshold to distinguish data between benign and deleterious (RF Score Only) (Min: 0 / Max: 1)
Use Default Value
(Default: 0.6 )
population
1000g
threshold
*
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
Use Default Value
(Default: 0.05 )
exac
threshold
*
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
Use Default Value
(Default: 0.05 )
esp6500
threshold
*
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
Use Default Value
(Default: 0.05 )
gnomad_exome
threshold
*
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
Use Default Value
(Default: 0.05 )
gnomad_genome
threshold
*
Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1)
Use Default Value
(Default: 0.05 )
prediction
revel
weight
*
Weight of this database
Use Default Value
(Default: 1.9262 )
sift
weight
*
Weight of this database
Use Default Value
(Default: 0.9924 )
polyphen2_hdiv
weight
*
Weight of this database
Use Default Value
(Default: 0.9228 )
polyphen2_hvar
weight
*
Weight of this database
Use Default Value
(Default: 1.0794 )
mutation_taster
weight
*
Weight of this database
Use Default Value
(Default: 1.664 )
mutation_assessor
weight
*
Weight of this database
Use Default Value
(Default: 1.1849 )
vest3
weight
*
Weight of this database
Use Default Value
(Default: 1.4583 )
lrt
weight
*
Weight of this database
Use Default Value
(Default: 0.958 )
metasvm
weight
*
Weight of this database
Use Default Value
(Default: 1.0051 )
metalr
weight
*
Weight of this database
Use Default Value
(Default: 1.0468 )
cadd
weight
*
Weight of this database
Use Default Value
(Default: 1.0301 )
dann
weight
*
Weight of this database
Use Default Value
(Default: 0.964 )
fathmm_mkl
weight
*
Weight of this database
Use Default Value
(Default: 0.921 )
gerp
weight
*
Weight of this database
Use Default Value
(Default: 0.997 )
fathmm
weight
*
Weight of this database
Use Default Value
(Default: 1.3344 )
provean
weight
*
Weight of this database
Use Default Value
(Default: 1.1105 )
phastcons20way
weight
*
Weight of this database
Use Default Value
(Default: 0.9393 )
phastcons100way
weight
*
Weight of this database
Use Default Value
(Default: 1.0137 )
siphy
weight
*
Weight of this database
Use Default Value
(Default: 0.9098 )
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