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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
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