annovar mouse

[Robby]

Hi everyone,
I use annovar for SNP annotation in human and would like to use the summarize_annovar.pl script for mouse as well. Unfortunally the script does just accept hg18 and hg19 as input for the parameter buildver. Is there any possibility to use that script for annotation?
Thanks Robby

[swbarnes2]

I use it for mouse all the time. But you do have to download the mouse genome, and use buildver mm9.

[sophiespo]

Can someone please tell me how to achieve this? I use --buildver mm9 and I get this error:

Error in argument: the --buildver argument must be 'hg18' or 'hg19'

[rzeng]

Hi, I may have the same problem as yours

I use

[$ variants_reduction.pl snps.annovar mm10db/ -protocol nonsyn_splicing,genomicSuperDups,SC_MOUSE_GENOMES.genotype.vcf,dominant -operation g,rr,f,m -out reduce -buildver mm10 &

Error in argument: the --buildver argument must be 'hg18' or 'hg19']


[/CODE]

Can someone please tell me how to achieve this? I use --buildver mm9 and I get this error:

Error in argument: the --buildver argument must be 'hg18' or 'hg19'