--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 <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--discard-coalesced-snvs <Boolean> |
SNVs that have been coalesced into a longer variation will be discarded (default: true) |
--genetic-code <Genetic code> |
Genetic code used for annotating variants with amino acid changes (default: 1 Standard) |
-i, --input <ClcObjectUrl> |
Input data on server |
--ignore-broken-pairs <Boolean> |
(default: true) |
--ignore-nonspecific-matches <Boolean> |
(default: true) |
--ignore-quality-scores <Boolean> |
(default: false) |
--iontorrent-454-correction <Boolean> |
Indels found in homopolymer regions are ignored. (default: false) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--min-coverage |
|
Integer: >= 1 |
Variants covered by less than this number of reads will not be called. (default: 10) |
--ploidy |
|
Integer: 1 <= x <= 4 |
The maximum number of different alleles expected. (default: 2) |
--variant-in-forward-reverse-reads |
|
<Boolean> |
Variants should be supported by at least 5--variant-probability |
Double: 0.0 < x <= 100.0 |
The probability that the variant is different from the reference sequence. Lowering this number will detect more variants. (default: 90.0) |