<action type="shell_command">java -jar kggseq.jar --no-lib-check --resource-update  --resource resources --buildver hg19 --db-filter 1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all  --patho-gene-predict --dgv-cnv-annot --vcf-file examples-lite/rare.disease.hg19.vcf</action>


<action type="shell_command">java -Xmx4g -jar kggseq.jar --no-lib-check --no-qc --resource-update --resource resources --buildver hg19 --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action>







questa riga sottostante è l'unione delle due sopra e sarà quella definitiva


<action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all  --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10  --vcf-file examples-lite/rare.disease.hg19.vcf</action>