| Name | Enable? | Databases |
|---|---|---|
| filter |
|
|
| filter_score |
|
|
| info |
|
|
| cancer_somatic |
|
|
| population |
|
|
| prediction |
|
|
| unspecified |
|
| Group | Database | Argument name | Description | Value |
|---|---|---|---|---|
| filter | func_refgene | filter_list |
|
|
| filter | func_refgene | mode | 0: filtered if in filter_list | 1: filtered if not in filter_list | Keep variant if matched with filter_list |
| filter | exonic_refgene | filter_list |
|
|
| filter | exonic_refgene | mode | 0: filtered if in filter_list | 1: filtered if not in filter_list | REMOVE variant if matched with filter_list |
| filter | aachange | gene_name_list | Gene name that you wish to find (1 line per gene name) | (No value) |
| filter | aachange | refseq_list | Refseq accession number that you wish to find (1 line per number) | (No value) |
| filter | aachange | exon_list | Exon name that you wish to find (1 line per exon name) | (No value) |
| filter | aachange | coding_ref_list | Coding DNA reference sequence that you wish to find (1 line per refseq) | (No value) |
| filter | aachange | protein_ref_list | Protein reference sequence that you wish to find (1 line per refseq) | (No value) |
| filter_score | exonic_refgene_score | list | Determine which exonic function prefered to be seen first in the report. |
|
| filter_score | regsnpintron_disease | disease_mode | Mode of scoring | 0/0.5/1 (Benign/Possibly Damaging/Damaging) |
| filter_score | dbsc_snv_ada | threshold_ada | Specified threshold to distinguish data between benign and deleterious (ADA Score Only) (Min: 0 / Max: 1) | 0.6 |
| filter_score | dbsc_snv_rf | threshold_rf | Specified threshold to distinguish data between benign and deleterious (RF Score Only) (Min: 0 / Max: 1) | 0.6 |
| population | 1000g | threshold | Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1) | 0.05 |
| population | exac | threshold | Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1) | 0.05 |
| population | esp6500 | threshold | Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1) | 0.05 |
| population | gnomad_exome | threshold | Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1) | 0.05 |
| population | gnomad_genome | threshold | Specified threshold to distinguish data between common and uncommon (Min: 0 / Max: 1) | 0.05 |
| prediction | revel | weight | Weight of this database | 1.9262 |
| prediction | sift | weight | Weight of this database | 0.9924 |
| prediction | polyphen2_hdiv | weight | Weight of this database | 0.9228 |
| prediction | polyphen2_hvar | weight | Weight of this database | 1.0794 |
| prediction | mutation_taster | weight | Weight of this database | 1.664 |
| prediction | mutation_assessor | weight | Weight of this database | 1.1849 |
| prediction | vest3 | weight | Weight of this database | 1.4583 |
| prediction | lrt | weight | Weight of this database | 0.958 |
| prediction | metasvm | weight | Weight of this database | 1.0051 |
| prediction | metalr | weight | Weight of this database | 1.0468 |
| prediction | cadd | weight | Weight of this database | 1.0301 |
| prediction | dann | weight | Weight of this database | 0.964 |
| prediction | fathmm_mkl | weight | Weight of this database | 0.921 |
| prediction | gerp | weight | Weight of this database | 0.997 |
| prediction | fathmm | weight | Weight of this database | 1.3344 |
| prediction | provean | weight | Weight of this database | 1.1105 |
| prediction | phastcons20way | weight | Weight of this database | 0.9393 |
| prediction | phastcons100way | weight | Weight of this database | 1.0137 |
| prediction | siphy | weight | Weight of this database | 0.9098 |