Configuration file - shengqh/glmvc GitHub Wiki
You need to define some program locations and parameter sets in the configuration file (glmvc.linux or glmvc.win)
<?xml version="1.0" encoding="utf-8"?>
<config>
<program name="annovar" command="table_annovar.pl" defaultparameterset="">
<parameterset name="hg19">
<parameter name="databasedir" default="/scratch/cqs/shengq1/references/annovar/humandb/" />
<parameter name="protocol" default="refGene,snp138,cosmic70" />
<parameter name="operation" default="g,f,f" />
</parameterset>
</program>
</config>
remember to change the annovar paramters to right one.