java -jar \$KGGSEQ_JAR_PATH/kggseq.jar
## Environmental settings
--buildver hg19
--resource \$KGGSEQ_JAR_PATH/resources
--no-lib-check
--no-resource-check
--no-progress-check
--out results
--o-vcf
--no-gz

--vcf-file $inputFile
--ped-file $pedFile
--db-gene $db_gene
$composite_subject_id

## Variant and genotype filters
#if str($variant_genotype_filters.variant_genotype_filters_select) == "yes"
  $variant_genotype_filters.pass_variant_only
  --seq-qual $variant_genotype_filters.seq_qual
  --seq-mq $variant_genotype_filters.seq_mq
  --seq-sb $variant_genotype_filters.seq_sb
  --seq-fs $variant_genotype_filters.seq_fs
  --min-heta $variant_genotype_filters.min_heta
  --min-homa $variant_genotype_filters.min_homa
  --min-hetu $variant_genotype_filters.min_hetu
  --min-homu $variant_genotype_filters.min_homu
  --min-obsa $variant_genotype_filters.min_obsa
  --min-obsu $variant_genotype_filters.min_obsu
  --min-obs $variant_genotype_filters.min_obs
  #if str($variant_genotype_filters.hwe_control)
    --hwe-control $variant_genotype_filters.hwe_control
  #end if
  #if str($variant_genotype_filters.hwe_case)
    --hwe-case $variant_genotype_filters.hwe_case
  #end if
  #if str($variant_genotype_filters.hwe_all)
    --hwe-all $variant_genotype_filters.hwe_all
  #end if
  --gty-qual $variant_genotype_filters.gty_qual
  --gty-dp $variant_genotype_filters.gty_dp
  --gty-sec-pl $variant_genotype_filters.gty_sec_pl
  --gty-af-ref $variant_genotype_filters.gty_af_ref
  --gty-af-het $variant_genotype_filters.gty_af_het
  --gty-af-alt $variant_genotype_filters.gty_af_alt
#else
  --no-qc
#end if

## Genetic inheritance
#if str($genetic_filters.genetic_filters_select) == "yes"
  #if str($genetic_filters.genetic_model.genetic_model_select) == "yes"
    #if $genetic_filters.genetic_model.custom_genetic_params
      --genotype-filter $genetic_filters.genetic_model.custom_genetic_params
    #end if
  #else
    $genetic_filters.genetic_model.suggested_genetic_params
  #end if
#end if

## Homozygosity - IBS - IBD filters
#if str($hom_ibs_ibd_filters.hom_ibs_ibd_filters_select) == "yes"
  #if str($hom_ibs_ibd_filters.homozygosity_case_filter)
    --homozygosity-case-filter $hom_ibs_ibd_filters.homozygosity_case_filter
  #end if
  #if str($hom_ibs_ibd_filters.ibs_case_filter)
    --ibs-case-filter $hom_ibs_ibd_filters.ibs_case_filter
  #end if
  #if str($hom_ibs_ibd_filters.ibd_annot) != 'None'
    --ibd-annot $hom_ibs_ibd_filters.ibd_annot
  #end if
#end if

## Gene feature filters
#if str($gene_feature_filters.gene_feature_filters_select) == "yes" and $gene_feature_filters.gene_features
  --gene-feature-in $gene_feature_filters.gene_features
  --splicing $gene_feature_filters.splicing
  --neargene $gene_feature_filters.neargene
#end if

## Common variants filters
#if str($allele_freq_filters.allele_freq_filters_select) == "yes"
  #if $allele_freq_filters.allele_freq_db
    --db-filter $allele_freq_filters.allele_freq_db
  #end if
  --rare-allele-freq $allele_freq_filters.rare_allele_freq
#end if

## Genomic regions filters
#if str($genomic_region_filters.genomic_region_filters_select) == "yes"
  $genomic_region_filters.ignore_indel_or_snv
  #if $genomic_region_filters.regions_in
    --regions-in "$genomic_region_filters.regions_in"
  #end if
  #if $genomic_region_filters.regions_out
    --regions-out "$genomic_region_filters.regions_out"
  #end if
  #if $genomic_region_filters.genes_in
    --genes-in "$genomic_region_filters.genes_in"
  #end if
  #if $genomic_region_filters.genes_out
    --genes-out "$genomic_region_filters.genes_out"
  #end if
  $genomic_region_filters.superdup
  #if str($genomic_region_filters.gene_var_filter)
    --gene-var-filter $genomic_region_filters.gene_var_filter
  #end if
#end if

## Predicted impact filters
#if str($impact_filters.impact_filters_select) == "yes"
  --db-score dbnsfp
  $impact_filters.filter_nondisease_variant
  $impact_filters.mendel_causing
#end if

## Add annotations
#if str($add_annotations.add_annotations_select) == "yes"
  #if str($add_annotations.o_flanking_seq)
    --o-flanking-seq $add_annotations.o_flanking_seq
  #end if
  $add_annotations.genome_annotation
  $add_annotations.omim_annotation
  $add_annotations.cosmic_annotation  
  $add_annotations.scsnv_annotation
  $add_annotations.dgv_cnv_annotation
  $add_annotations.superdup_annotation
  $add_annotations.mouse_pheno_annotation
  $add_annotations.zebrafish_pheno_annotation
  $add_annotations.ddd_annotation
  $add_annotations.patho_gene_predict_annotation  
  #if $add_annotations.pubmed_mining_gene
    --phenotype-term "$add_annotations.pubmed_mining_gene" --pubmed-mining
  #end if
  #if str($add_annotations.shared_genes.shared_genes_select) == "yes"
    --ppi-annot string
    --candi-file $add_annotations.shared_genes.candi_file
    --ppi-depth $add_annotations.shared_genes.ppi_depth
    --pathway-annot $add_annotations.shared_genes.pathway_annot
  #end if
#end if
> $logFile