Question: Error while trying ANNOVAR
0
gravatar for banerjeeshayantan
17 months ago by
banerjeeshayantan190 wrote:

I am trying to annotate a set of mice variants using annovar. I have used the command below:

perl table_annovar.pl C131T137.avinput mousedb/ -buildver mm10 -out myanno -remove -protocol refGene  -operation g

But I am getting the following error
Error:

FASTA sequence file mousedb/mm10_refGeneMrna.fa does not exist. Please use 'annotate_variation.pl --downdb refGene mousedb' download the database.
Error running system command: <annotate_variation.pl -geneanno -buildver mm10 -dbtype refGene -outfile myanno.refGene -exonsort C131T137.avinput mousedb/>

I downloaded the mousedb as suggested in the command above but still there is the above error. Where am I going wrong?

annovar • 616 views
ADD COMMENTlink written 17 months ago by banerjeeshayantan190

Output of ls inside that mousedb folder?

ADD REPLYlink modified 17 months ago • written 17 months ago by ATpoint41k

I changed the name of the ref genome file to mm10_refGeneMrna.fa and the program ran. I hope I did it correctly. But the output of the annotated file tells whether the variant is exonic/intergenic etc. How do I get the sift/polyphen scores for each variant?

ADD REPLYlink modified 17 months ago • written 17 months ago by banerjeeshayantan190
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