#one argument per line 
#Enviromental setting
--buildver hg18 \ 
--resource ./resources \  

#Specify the input files
--vcf-file  examples/complex.disease.vcf.hg18.vcf \ 
--ped-file examples/complex.disease.ped.txt \ 
--composite-subject-id

#Output setting
--excel \
--out kggseqtest0808_2 \
--o-vcf \  
--o-plink-ped \
--o-ked \

#QC
--gty-qual 10 \ 
--gty-dp 4 \  
--gty-af-ref 0.05 \  
--gty-af-alt 0.25 \  
--disable-vcf-filter \  
--seq-qual 50 \ 
--seq-mq 20 \
--seq-sb 0 \
--min-obsa 1 \
--min-obsu 1 \
--min-obs 3  \

#Filtering and Prioritization 
--filter-model case-unique \ 
--db-gene refgene \ 
--gene-feature-in 0,1,2,3,4,5,6,7,8,9,10 \ 
--db-filter hg18_1kgasn2010,hg18_1kgeur2010,hg18_dbsnp130,hg18_dbsnp129 \ 
--allele-freq 0.01 0.99 \ 
--db-score dbnsfp \ 
--ignore-indel \ 

#Annotation
--genome-anot \  
--candi-list HLA-DPA1,HLA-DPB1 \
--pathway-annot cura \  
--ppi-annot string \ 
--ppi-depth 1 \  
--pubmed-mining Crohn's+disease,Inflammatory+bowel+disease \ 

#Plotting
#--mafplot \