how to generate setID file?

Question

[la.sy]

i want to generate setID file for SKAT(r package)

so i use "annovar"

but i don't know how to use annovar after i read guide

could anyone provide me some suggestion

[NB]

what exactly are you not understanding ? The annovar documentation is quite straight forward. Alternatively, try wANNOVAR

Answer 1

[mer.tantawy]

I know this is for a long time, but I found till now there is no clear answer

so to use annovar firstly you download annovar from this link https://annovar.openbioinformatics.org/en/latest/ and then in your Linux unzip the file tar xvfz annovar.latest.tar.gz then module load annovar then run this annotate_variation.pl -out ex1 -build hg19 example/ex1.avinput humandb/ as an example to understand what is happening here, all the examples files will be downloaded automatically

marwa