Error while trying ANNOVAR
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?
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Output of
lsinside thatmousedbfolder?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?