--ambiguity-noise-minimum |
|
Integer: >= 1 |
The minimum number of reads to support a base to be included. Otherwise the base is considered noise. NOTE: This filter is unaffected by the "Use quality score" option. (default: 1) |
--ambiguity-noise-threshold |
|
Double: 0.0 <= x <= 1.0 |
When reads mapped to the same position disagrees on the base, this option defines when the difference is to be interpreted as noise and when there is an actual ambiguity. When this option is set to X, then any base, that is mapped to a given position with a frequency less than X at that particular position, is considered noise and will not contribute to calling the ambiguity code. NOTE: When "Use quality score" is enabled, accumulated quality scores are used instead of raw read coverage for this filter. (default: 0.1) |
--annotate-consensus-sequence <Boolean> |
Annotate consensus sequence. Annotations are: "Conflict" for positions with a conflict, "Deletion" for positions where a gap is called while the reference has a non-gap "Insertion" where a non-gap is called while the reference has a gap"Removal" for positions removed by low coverage, and/orpositions where filtering before resolving conflicts leaves no data to peform the resolution"Ambiguous base" for positions with an ambiguous consensus symbol"Misc. difference" for every position where the consensus is different from the reference (default: false) |
--conflict-handling <[VOTE, AMBIGUITY_CODE]> |
Select a strategy for handling conflicting reads (default: VOTE) |
-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 |
--keep-consensus-annotations <Boolean> |
Keep the annotations already on the consensus sequence (default: true) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--low-coverage-handling <[REMOVE, INSERT_N, FILL_FROM_REFERENCE]> |
Define low coverage regions and how to handle such regions (default: INSERT_N) |
--low-coverage-removal-handling <[CONCATENATE, SPLIT]> |
Split sequence into subsequences of multiple covered sequences or concatenate the resulting covered sequences to produce a single consensus sequence. (default: SPLIT) |
--low-coverage-threshold |
|
Integer: 0 <= x <= 2147483647 |
Specify the maximum number of reads in a region of low coverage. The default value '0' means that only regions with no coverage are considered low coverage while values n>0 means that regions with up to n reads mapped will still be considered low coverage. Below, you can select how to handle low coverage regions (default: 0) |
--transfer-reference-annotations <Boolean> |
Transfer annotations from the reference sequence (default: false) |
--use-quality-scores <Boolean> |
Quality scores will be used if available instead of raw read counts when calling the consensus symbol, see the manual for details. NOTE: The semantics of ambiguity code filter "Noise threshold" is affected by enabling/disabling this option when quality scores are available. (default: false) |
