--create-coverage-graph <Boolean> |
Create coverage graph (default: false) |
--create-coverage-table <Boolean> |
Create coverage table (default: false) |
--create-report <Boolean> |
Create report (default: true) |
--create-track <Boolean> |
Create track (default: true) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
-i, --input <ClcObjectUrl> |
Input data on server |
--ignore-broken-pairs <Boolean> |
When ticked, broken pair reads will be ignored. (default: true) |
--ignore-nonspecific-matches <Boolean> |
When ticked, reads that match in several places will be ignored. (default: true) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--min-coverage <Integer> |
Minimum coverage needed on all positions in a target, in order for that target to be considered covered (default: 30) |
--report-type <[DEFAULT_COVERAGE_TYPE, DEFAULT_COVERAGE_TYPE_II, DEFAULT_COVERAGE_TYPE_III, LOW_COVERAGE_TYPE, HIGH_COVERAGE_TYPE]> |
Defines the boundaries of the coverage tables (default: DEFAULT_COVERAGE_TYPE) |
--target-regions <ClcObjectUrl> |
Select track of target regions |
