This tool can be used to filter the ranked results using basic query (initial) or ADVACED QUERY box using MySQL commands. Sample SQL queries are provided below and can be copy-pasted in the advanced query box. The user can use build queries using regular expressions, exact keywords for filtering by each column of the result.


Operator description:
LIKE filter for variants exactly EQUAL to [query]
NOT LIKE filter for variants exactly NOT EQUAL to [query]
REGEXP using regular expressions
IS NULL/IS NOT NULL field is not empty (can be used only in ADVANCED QUERY)
= Equal to function
> Greater than function
>= Greater than Equal to function
< Less than function
<= Less than Equal to function
!= Not equal to function
EXAMPLE FILTERING STEPS USING RESULT EXPLORER.

Use ADVACED QUERY option for examples below. Users can copy-paste QUERY into the advanced query box (excluding term WHERE). We advice filtering using each category and examining results categorically.

FILTERQUERY
GWASCatalog gwasCatalog NOT LIKE 'NA'
CLINVAR clinvar_20140929 NOT LIKE 'NA'
1000g MAF <= 0.01 (rare variants) WHERE (1000g2014sep_eur <= '0.01' OR 1000g2014sep_eur = 'NA')
1000g MAF >= 0.05 (common variants) WHERE ( 1000g2014sep_eur >= '0.05')
Identify splicing, nonsynonymous, stopgain/stoploss
variants from RefSeq (excludes synonymous)
WHERE (Func_refGene REGEXP 'exonic|splic' AND
ExonicFunc_refGene REGEXP '(nonsyno)|(stop)|(NA)')
Identify splicing, nonsynonymous, stopgain/stoploss
variants from RefSeq (exclude ncRNA_exonic)
WHERE (Func_refGene REGEXP '(^exonic)|splic' AND
ExonicFunc_refGene REGEXP '(nonsyno)|(stop)|(NA)')
Filter MAF > 0.01 in 1000g WHERE (1000g2014sep_eur <= '0.01' OR 1000g2014sep_eur = 'NA')
Filter MAF > 0.01 in ESP600 WHERE (esp6500_ea <= '0.01' OR esp6500_ea = 'NA')
Filter MAF > 0.01 in ExAC WHERE (exac03 <= '0.01' OR exac03 = 'NA')
ALL in one step (using refGene as reference db):

(i)Identify splicing, nonsynonymous, stopgain/stoploss
variants
(ii)Filter MAF > 0.01 in 1000g
(iii)Filter MAF > 0.01 in ESP600
(iv)Filter MAF > 0.01 in ExAC
WHERE ( ( Func_refGene REGEXP '(^exonic)|splic' AND ExonicFunc_refGene REGEXP '(nonsyno)|(stop)|(NA)' ) AND ( 1000g2014sep_eur <= '0.01' OR 1000g2014sep_eur = 'NA' ) AND ( esp6500_ea <= '0.01' OR esp6500_ea = 'NA' ) AND ( exac03 <= '0.01' OR exac03 = 'NA' ) )


The following Variant Filtering Categories can be used for the filtering process:

Variant Category Description
exonicvariant overlaps a coding
splicingvariant is within 2-bp of a splicing junction
ncRNAvariant overlaps a transcript without coding annotation in the gene definition
UTR5variant overlaps a 5' untranslated region
UTR3variant overlaps a 3' untranslated region
intronicvariant overlaps an intron
upstreamvariant overlaps 1-kb region upstream of transcription start site
downstreamvariant overlaps 1-kb region downtream of transcription end site
intergenicvariant is in intergenic region
Exonic CategoryDescription
stopgainSNV that leads to the immediate creation of stop codon at the variant site.
stoplossSNV that leads to the immediate elimination of stop codon at the variant site
nonsynonymous SNVa single nucleotide change that cause an amino acid change
synonymous SNVa single nucleotide change that does not cause an amino acid change
unknownunknown function (due to various errors in the gene structure definition in the database file)