--control-mappings <ClcObjectUrl> |
A number of read mappings, to be used as control cases. Gender-matched controls are optimal. |
--create-algorithm-report <Boolean> |
Create algorithm report, which contains advanced details about the statistical models used in the algorithm (default: true) |
--create-target-track <Boolean> |
Create a target-level CNV track, containing calls for individual CNV targets (default: true) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--enforce-small-region-sensitivity <Boolean> |
Greatly increases the sensitivity of the prediction of very small CNVs, leading to a higher number of predicted CNVs, but also increasing the false positive rate. (default: false) |
--gene-track <ClcObjectUrl> |
If given, this gene track will be used for producing gene-level CNV results. |
--graining-level <[COARSE, INTERMEDIATE, FINE]> |
Graining level for the prediction of CNV regions (default: COARSE) |
-i, --input <ClcObjectUrl> |
Input data on server |
--ignore-broken-pairs <Boolean> |
Paired reads that have been broken up and mapped individually will be ignored (default: true) |
--ignore-nonspecific-matches <Boolean> |
Reads that match in several places will be ignored (default: true) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--low-coverage-cutoff |
|
Integer: 0 <= x <= 2147483647 |
Targets with coverage below this number will be considered low-coverage and will not be used to calculate the statistical models (default: 30) |
--minimum-fold-change-magnitude |
|
Double: 0.0 <= x < Infinity |
The minimum fold-change magnitude to call a 'strong' CNV signal (default: 1.4) |
--significance-level |
|
Double: 0.0 <= x <= 1.0 |
A CNV will be called if the corrected p-value is less than or equal to this value (default: 0.05) |
--target-track <ClcObjectUrl> |
The targeted regions in the analysis |
