consensus_sequence_extraction

--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. (default: 0.1)
--annotate-consensus-sequence <Boolean> Annotate consensus sequence for low coverage regions or ambiguities (default: true)
--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
--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 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>
Integer: 0 <= x <= 2147483647 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)
--use-quality-scores <Boolean> If present, quality scores will be used as weights on the votes in voting. (default: false)