155 <option value="refgene" selected="true">refgene: The RefGene database compiled by UCSC from hg19 refGene. Note: RefSeq has NO mitochondria gene definition</option>
156 <option value="gencode">gencode: The GENCODE gene sets. Note: GENCODE contains similar number of coding genes but more transcripts than RefGene. It HAS the mitochondria gene definition</option>
169 <param name="pass_variant_only" type="boolean" truevalue="--vcf-filter-in PASS" falsevalue="" checked="true" label="Don't include filtered loci (--vcf-filter-in PASS)" help="Keep only variants with FILTER equal to PASS" />
175 <param name="min_homa" type="integer" value="0" label="Minimal observed number of alternate homozygote genotypes in cases (the affected) (--min-homa)" />
176 <param name="min_hetu" type="integer" value="0" label="Minimal observed number of heterozygote genotypes in controls (the unaffected) (--min-hetu)" />
177 <param name="min_homu" type="integer" value="0" label="Minimal observed number of alternate homozygote genotypes in controls (the unaffected) (--min-homu)" />
179 <param name="min_obsu" type="integer" value="0" label="Minimal observed number of non-missing genotypes in controls (the unaffected) (--min-obsu)" />
181 <param name="hwe_control" type="float" value="" optional="true" label="Exclude variants in controls with the Hardy-Weinberg test p-value <= this value (--hwe-control)" />
182 <param name="hwe_case" type="float" value="" optional="true" label="Exclude variants in cases with the Hardy-Weinberg test p-value <= this value (--hwe-case)" />
183 <param name="hwe_all" type="float" value="" optional="true" label="Exclude variants in all subjects with the Hardy-Weinberg test p-value <= this value (--hwe-all)" />
187 <param name="gty_af_ref" type="float" value="0.05" label="Maximal fraction of reads carrying alternative allele at a reference allele homozygous genotype (--gty-af-ref)" />
188 <param name="gty_af_het" type="float" value="0.25" label="Minimal fraction of reads carrying alternative allele at a heterozygous genotype (--gty-af-het)" />
189 <param name="gty_af_alt" type="float" value="0.5" label="Minimal fraction of reads carrying alternative allele at a alternative allele homozygous genotype (--gty-af-alt)" />
226 <option value="--unique-gene-filter">Only genes on which EVERY affected subject has at least one case-unique alternative allele, but these alleles may be from different variants (--unique-gene-filter)</option>
241 <param name="homozygosity_case_filter" type="integer" value="" optional="true" label="Filter by Runs of Homozygosity (ROH) (--homozygosity-case-filter)" help="Minimal length (in kb) of consecutive homozygous genotype for each interesting variant" />
242 <param name="ibs_case_filter" type="integer" value="" optional="true" label="Filter by Identical by State (IBS) (--ibs-case-filter)" help="Minimal length (in kb) of the region in which there is at least one allele identical among all cases" />
243 <param name="ibd_annot" type="data" format="txt,tabular,bed" optional="true" label="Add Identical by Descent (IBD) annotation (--ibd-annot)" help="File with IBD or significant linkage regions. Variants within these regions will be highlighted. Note: title line CHR START END is needed" />
255 <param name="gene_features" type="select" display="checkboxes" multiple="true" label="Select gene features (--gene-feature-in)" help="Variants falling outside the selected regions will be excluded">
275 <param name="splicing" type="integer" value="2" label="Window size in base-pair around the splicing junction to flag the variant as splicing (--splicing)" />
289 <option value="1kgeur201305">1KG EUR 201305: 495 subjects in the EUR panel of 1000 Genomes Project release in 2013 May (around 24.0 million sequence variants)</option>
290 <option value="1kgeas201305">1KG EAS 201305: 496 subjects in the EAS panel of 1000 Genomes Project release in 2013 May (around 23.5 million sequence variants)</option>
291 <option value="1kgafr201305">1KG AFR 201305: 645 subjects in the AFR panel of 1000 Genomes Project release in 2013 May (around 41.7 million sequence variants)</option>
292 <option value="1kgsas201305">1KG SAS 201305: 485 subjects in the SAS panel of 1000 Genomes Project release in 2013 May (around 26.7 million sequence variants)</option>
293 <option value="1kgamr201305">1KG AMR 201305: 346 subjects in the AMR panel of 1000 Genomes Project release in 2013 May (around 28.2 million sequence variants)</option>
304 <option value="dbsnp138nf">dbSNP 138nf: dbSNP version 138 without the flagged SNPs by UCSC. Flagged SNPs include SNPs clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%</option>
307 <option value="exac">Exome Aggregation Consortium (ExAC): Variants from 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies</option>
308 <option value="gadexome">Genome Aggregation Database - Exome (gnomAD): Variants from 123,136 exomes sequenced as part of various disease-specific and population genetic studies</option>
309 <option value="gadgenome">Genome Aggregation Database - Genome (gnomAD): Variants from 15,496 whole-genomes sequenced as part of various disease-specific and population genetic studies</option>
311 <param name="rare_allele_freq" type="float" value="0.01" label="Minor allele frequency (MAF) for selecting rare variants (--rare-allele-freq)" help="Set to >1 to only annotate MAF, without filtering" />
328 <param name="regions_in" type="text" label="Keep only variants within some genomic regions (--regions-in)" help="A comma-separated list of genomic regions, e.g. chrX,chrY:1-1000" />
329 <param name="regions_out" type="text" label="Ignore variants within some genomic regions (--regions-out)" help="A comma-separated list of genomic regions, e.g. chrX,chrY:1-1000" />
330 <param name="genes_in" type="text" label="Keep only variants within some genes (--genes-in)" help="A comma-separated list of gene symbols, e.g. TCF4,CNNM2,ANK3" />
331 <param name="genes_out" type="text" label="Ignore variants within some genes (--genes-out)" help="A comma-separated list of gene symbols, e.g. TCF4,CNNM2,ANK3" />
332 <param name="superdup" type="select" label="Annotate or filter out variants in super duplicate regions?" help="As defined in genomicSuperDups dataset from UCSC">
337 <param name="gene_var_filter" type="integer" value="" optional="true" label="Filter out genes with at least this number of putative pathogenic variants (--gene-var-filter)" help="As a rule of thumb, it is safe to set a cutoff of 4 or more. " />
368 <param name="superdup_annotation" type="boolean" truevalue="--superdup-annot" falsevalue="" checked="true" label="Mark the variants in the super duplicate regions (--superdup-annot)" />
369 <param name="mouse_pheno_annotation" type="boolean" truevalue="--mouse-pheno" falsevalue="" checked="true" label="Annotate the genes with known mouse phenotypes as reference (--mouse-pheno)" />
370 <param name="zebrafish_pheno_annotation" type="boolean" truevalue="--zebrafish-pheno" falsevalue="" checked="true" label="Annotate the genes with known zebrafish phenotypes as reference (--zebrafish-pheno)" />
373 <param name="pubmed_mining_gene" type="text" label="Text mining in PubMed: search term(s) of interest (e.g. disease name)" help="A comma-separated list of search terms, each composed by plus-separated words, e.g. spinocerebellar+ataxia,other+search+term. If empty, no search will be performed" />
382 <param name="ppi_depth" type="integer" value="1" label="Maximum distance of a protein-protein interaction (PPI) between candidate genes and genes containing the variants (--ppi-depth)" />
383 <param name="pathway_annot" type="select" label="Select databases for the identification of shared pathways between candidate genes and genes containing the variants (--pathway-annot)" help="Gene sets are extracted from MSigDB">
436 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
