annotations using annovar

MayaAM · 01-02-2013, 06:09 AM

Hello,
I'm using annovar to annotate variants in exome analysis.

I've noticed that a lot of genes that can be found in the gff of the genome (I'm using hg19), are missing in the annovar output.
In other words, annovar doesn't annotate a lot of variants located at positions that are inside exons according to the gff.

Which files in annovar database are the genes?
How can I know the origin of annovar's gene database?
Is there a way to create a database for annovar instead of downloading it?
I also will be gald to know if anyone else encountered this.

Thank you,
Maya

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01-02-2013, 06:09 AM	#1
MayaAM Junior Member Location: Israel Join Date: Jun 2012 Posts: 4	annotations using annovar Hello, I'm using annovar to annotate variants in exome analysis. I've noticed that a lot of genes that can be found in the gff of the genome (I'm using hg19), are missing in the annovar output. In other words, annovar doesn't annotate a lot of variants located at positions that are inside exons according to the gff. Which files in annovar database are the genes? How can I know the origin of annovar's gene database? Is there a way to create a database for annovar instead of downloading it? I also will be gald to know if anyone else encountered this. Thank you, Maya