#one argument per line 
#Enviromental setting
--buildver hg19 \ 
--resource ./resources \  

#Specify the input files
--vcf-file examples/rare.disease.hg19.vcf \ 
--ped-file examples/rare.disease.ped.txt  \ 


#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 \  
--vcf-filter-in PASS \  
--seq-qual 50 \ 
--seq-mq 20 \ 
--seq-sb 0 \ 
--min-obsa 1 \ 
--min-obsu 1 \ 

 #Filtering and Prioritization 
--genotype-filter 3,4,5,6  \ 
--ibs-case-filter 1000 \ 
--db-gene refgene \ 
--gene-feature-in 0,1,2,3,4,5 \ 

--db-filter hg19_1kg201204,hg19_dbsnp137,hg19_ESP6500AA,hg19_ESP6500EA \ 
--db-filter-hard dbsnp138nf
--rare-allele-freq 0.006 \ 
--db-score dbnsfp \ 
--filter-nondisease-variant \
--regions-out chrX,chrY \ 

#Annotation
--genome-anot \  
--candi-list ECEL1,MYBPC1,TNNI2,TNNT3,TPM2 \ 
--pubmed-mining Arthrogryposis,Arthrogryposis+multiplex+congenita \ 

--pathway-annot cura \  
--ppi-annot string \
--ppi-depth 1 \