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)