Question: Annovar And Avsift, Column Error
2
gravatar for dahlo.mix1
7.3 years ago by
dahlo.mix120
Sweden
dahlo.mix120 wrote:

Hi there

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?

annovar • 2.4k views
ADD COMMENTlink written 7.3 years ago by dahlo.mix120

Can you post the first lines of the hg19annovardb/hg19_avsift.txt file?

ADD REPLYlink written 7.3 years ago by Niek De Klein2.5k

1 14696 14696 C A 0.41 * Y 1 14696 14696 C G 0.41 * Y 1 14697 14697 T A 0.96 * L 1 14697 14697 T C 0.1 * W

pastebin, if it looks weird here: http://pastebin.com/3qL0UskX

ADD REPLYlink written 7.3 years ago by dahlo.mix120
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