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

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

#Output setting
--out ./test0808_1 \ 
--excel \ 
--o-seattleseq \  
--o-vcf \  
#--o-flanking-seq 50 \ 
 
#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 0 \ 

#Filtering and Prioritization 
--genotype-filter 3 \ \ 
--ibs-check \ 
--db-gene refgene \ 
--gene-feature-in 0,1,2,3,4,5 \ 
--db-filter hg18_1kgasn2010,hg18_1kgeur2010,hg18_dbsnp130,hg18_ESP5400 \ 
--rare-allele-freq 0.006 \ 
--db-score dbnsfp \ 
--filter-nondisease-variant \ 
--regions-out chrX,chrY \ 

#Annotation
--genome-anot \  
--candi-list ATXN1,ATXN2,ATXN8OS,ATXN8,ATXN10,TTBK2 \ 
--pathway-annot cura \  
--ppi-annot string \ 
--ppi-depth 1 \  
--pubmed-mining Spinocerebellar+ataxia \