I tried to use Annovar to annotate my snps, but i can't get it to work. I can't even annotate the example file that follows with the program. The version of Annovar i'm running is from 2012-02-23.
# download the avsift database $ annotate_variation.pl -downdb -buildver hg19 avsift hg19_annovar_db/ # run annovar on the example file, ex1.human $ annotate_variation.pl -buildver hg19 -dbtype avsift ex1.human hg19_annovar_db/ NOTICE: The --geneanno operation is set to ON by default NOTICE: The --sift_threshold is set as 0.05 by default NOTICE: Reading gene annotation from hg19_annovar_db/hg19_avsift.txt ... Error: invalid record in hg19_annovar_db/hg19_avsift.txt (>=11 fields expected in avsift gene definition file): <1 14696 14696 C A 0.41 * Y>
Has there been any changes to the avsift format, or am I just making some trivial mistake?