I used the ANNOVAR command line
annotate_variation.pl -downdb -buildver hg19 refGene humandb
to download hg19_refGene.txt from UCSC and I'll use this database to create the input file for ANNOVAR in format http://www.openbioinformatics.org/annovar/annovar_filter.html#generic but all information I can get for the refGene format is from http://genome.ucsc.edu/FAQ/FAQformat
(
string geneName; "Name of gene as it appears in Genome Browser."
string name; "Name of gene"
string chrom; "Chromosome name"
char[1] strand; "+ or - for strand"
uint txStart; "Transcription start position"
uint txEnd; "Transcription end position"
uint cdsStart; "Coding region start"
uint cdsEnd; "Coding region end"
uint exonCount; "Number of exons"
uint[exonCount] exonStarts; "Exon start positions"
uint[exonCount] exonEnds; "Exon end positions"
)
which is not sufficient because the downloaded refGene has more columns. For example
1475 NM_000039 chr11 - 116706468 116708338 116706523 116708103 4 116706468,116707716,116708060,116708320, 116707127,116707873,116708123,116708338, 0 APOA1 cmpl cmpl 2,1,0,-1,
I tried to look many place to find the meaning of the last 6 columns. Anyone here can give the site that can explain the meaning of those columns?
as far as i can see in curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.sql"
`bin` smallint(5) unsigned NOT NULL,
`name` varchar(255) NOT NULL,
`chrom` varchar(255) NOT NULL,
`strand` char(1) NOT NULL,
`txStart` int(10) unsigned NOT NULL,
`txEnd` int(10) unsigned NOT NULL,
`cdsStart` int(10) unsigned NOT NULL,
`cdsEnd` int(10) unsigned NOT NULL,
`exonCount` int(10) unsigned NOT NULL,
`exonStarts` longblob NOT NULL,
`exonEnds` longblob NOT NULL,
`score` int(11) default NULL,
`name2` varchar(255) NOT NULL,
`cdsStartStat` enum('none','unk','incmpl','cmpl') NOT NULL,
`cdsEndStat` enum('none','unk','incmpl','cmpl') NOT NULL,
`exonFrames` longblob NOT NULL,
all the fields you need are present in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz
you just need to remove the some columns (bin...)
Hi Pierre,
How to create RefGene file for virus using annovar
•
written
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bioinforesearchquestions
Under "describe table schema" is the complete and right description:
you can visit http://genome.ucsc.edu/cgi-bin/hgTables and then click "describe the schema" button, the you can see the RefSeq gene predictions format.
Log in to answer this question.
The format description has been updated: http://genome.ucsc.edu/FAQ/FAQformat#format9
But it is still wrong: before name there is an something non-unique called bin and the uint id is the score.
Looks like there was no primary key for the data then.