--create-table <Boolean> |
Create table with annotated variants (default: false) |
--create-track <Boolean> |
Create a track of variants, useful for further analysis (default: true) |
-d, --destination <ClcUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--enable-advanced <Boolean> |
Enable advanced significance settings: maximum coverage, and sufficient and required supporting read count thresholds. (default: false) |
--genetic-code <Genetic code> |
Genetic code used for annotating variants with amino acid changes (default: 1 Standard) |
-i, --input <ClcUrl> |
Input data on server |
--ignore-broken-pairs <Boolean> |
(default: true) |
--ignore-nonspecific-matches <Boolean> |
(default: true) |
--iontorrent-454-correction <Boolean> |
Indels found in homopolymer regions are ignored. (default: false) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--max-coverage |
|
Integer: >= 1 |
Variants covered by more than this number of reads will not be called. (default: 99999) |
--max-gaps-and-mismatches |
|
Integer: >= 0 |
Any read where the neighborhood of a candidate variant contains more than this number of gaps and mismatches is considered of low quality and ignored for that variant. Must be at most twice the neighborhood radius. (default: 2) |
--min-central-quality |
|
Byte: 0 <= x <= 64 |
Applies only to reads that have quality scores. Any read where the bases included in a candidate variant have average quality score less than this number is considered of low quality and ignored for that variant. (default: 20) |
--min-coverage |
|
Integer: >= 1 |
Variants covered by less than this number of reads will not be called. (default: 10) |
--min-neighborhood-quality |
|
Byte: 0 <= x <= 64 |
Applies only to reads that have quality scores. Any read where the bases in the neighborhood of a candidate variant have average quality less than this number is considered of low quality and ignored for that variant. (default: 15) |
--min-read-freq |
|
Double: 0.0 < x <= 100.0 |
Variants with a frequency less than this number will not be called. (default: 35.0) |
--neighborhood-radius |
|
Integer: >= 0 |
The radius of the neighborhood considered for each read to assess read quality around a candidate variant position. The number of read residues considered will be twice the neighborhood radius. (default: 5) |
--ploidy |
|
Integer: >= 1 |
The maximum number of alleles expected for each variant. This should be equal to the ploidy of the sequenced genome, eg. 2 for a diploid organism. (default: 2) |
--required-read-count |
|
Integer: >= 1 |
Variants whose supporting read count is less than this number will not be called. (default: 1) |
--sufficient-read-count |
|
Integer: >= 1 |
Variants whose supporting read count is at least this number will be called irrespective of the minimum frequency setting. (default: 5) |
--variant-in-forward-reverse-reads |
|
<Boolean> |
Variants should be supported by at least 5 |